If the auction ended and I paid before the retail buyer purchased the domain, am I not the owner
That would depend on the terms of auction to which you agreed.
The answer to most questions of the variety of "I had X happen at an online service provider, what are my rights?" is usually "it depends on the terms offered" to a first approximation. If there are situations which aren't covered by the terms, then the situation is a little more interesting.
However, the entire context of this question is firmly in the realm of 'what do the relevant contracts say', as far as figuring out what an answer might be.
I realize nobody reads them, but it is often the case that someone will call or write to me and ask a question about an issue that came up in the context of a transaction with some online service provider. The usual problem is that it is going to take me 30 to 45 minutes to understand the issue, and then go off to read the relevant terms of service to determine what, if any, bearing they might have on the problem.
So, in this example, since there is one and only one Google result for the phrase "may cancel an auction if the domain being auctioned is sold to a retail buyer through the retail marketplace" - we can review the clause in context.
That section of the Agreement has two clauses:
---------------
9.1 Termination Rights
- Atom.com reserves the right to cancel or terminate any auction at its discretion, especially in cases of suspected fraud, technical malfunctions, or violations of these terms or Atom.com’s Platform Terms & Conditions.
- Additionally, Atom.com may cancel an auction if the domain being auctioned is sold to a retail buyer through the retail marketplace
-------------------
I added bold to that first part because, at the end of the day, their terms state that they claim the right to cancel or terminate any auction at their discretion.
The fact that they go on to list example scenarios like "especially" in cases of abuse, or if a retail sale happens, does not negate the fact that this contract says they can cancel any auction at their discretion.
So, I don't think focusing on whether the domain is "being auctioned" at the time of the retail sale really matters, since, if we are going by those terms, then they can cancel the auction anyway which, at least to me, suggests the ability to cancel one which has concluded as well.
Another point worth mentioning is that these are not all of the terms. The Auction Terms purport to incorporate the general platform terms at:
https://www.atom.com/Terms&Conditions
However, the general terms seem a little sketchy:
But, using an archived version, with the caveat that it may have been revised since the archive date, it's worth pointing out a couple of things...
https://web.archive.org/web/20240908222650/https://www.atom.com/Terms&Conditions
E. Subject to this Section, you agree that Atom and its third party providers will not be liable in respect of any claim by you (whether contractual, tortious, statutory or otherwise) for any direct, special, incidental, indirect, punitive, exemplary or consequential damages or injury including, but not limited to, any loss of profits, contracts, revenue or data arising out of or in connection with the provision of the Services or the provision of any other goods or services under this Agreement and whether as a result of any breach or default by, or any negligence of, Atom or its third party providers.
F. The maximum liability of Atom under this Agreement for any and all breaches of this Agreement and for any negligence in relation to this Agreement or Services, will not exceed the lesser of the amount you paid for Services, if any, for the event giving rise to Atom’s liability or $100.
....
16. Informal Dispute Resolution
In the event you have any dispute with us related to the Site, Services, and/or these Terms, you shall first try in good faith to settle such dispute by providing written notice to us describing the facts of the dispute (including any relevant documentation) and allowing us thirty (30) days to respond before initiating any formal dispute resolution proceeding. Notices to us must be sent by mail to 2000 Center Dr, Suite East C221, Hoffman Estates IL 60192. We will send any dispute related notice to you at the contact information we have for you. If for some reason the dispute is not resolved satisfactorily within thirty (30) days after receipt, any further dispute resolution will occur according to the provisions below. Engaging in this informal dispute resolution process is a requirement that must be fulfilled before commencing a formal dispute resolution proceeding, such as an arbitration or small claims court proceeding.
17. Arbitration Agreement & Waiver of Certain Rights
Except as set forth below, you and we agree that we will resolve any controversies, claims, counterclaims, or other disputes between you and us or you and a third-party agent of ours (each a “Claim”) through binding and final arbitration, instead of through court proceedings, in accordance with the Consumer Arbitration Rules of the American Arbitration Association (“AAA Rules”).
----------------------
After then finding the relevant "you're screwed" section of the contract, understanding that in order to bring a dispute, you must first mail your issue to a rented office in Illinois wait thirty days, and then give them another five days warning before initiating an arbitration under the rules of the AAA, I will generally ask something along the lines of:
"Do you want to try for the whole $100 or just part of it?"
As to your question, does "the auction" end before payment is made and a domain is transferred? If those steps are not part of the auction what are they?
But, if it wasn't for the terms under which they can do whatever they want and your best recovery is $100, you can look to other parts of the terms to decide how this contract defines when an auction is ended, for example:
2. Definitions
Auction: A timed event where a domain name is offered for sale to the highest bidder
This appears to define "Auction" as a timed event where a domain name is offered for sale to the highest bidder. So, after the bidding has concluded, it is no longer a "timed event" where the name remains offered.
So, clearly the auction had ended by that point. This interpretation is further reinforced by:
6.2 Payment Terms
The winning bidder has 72 hours from the close of the auction to make the payment for the winning bid.
where the implication seems to be that the "close of the auction" is when bidding ends, and that payment is made during a post-auction period. One could, I suppose, argue that the payment and fulfillment steps remain as, somehow, part of what is defined as the "auction", but the contract language is more consistent with the auction concluding at the end of bidding.
But, as a general point, if you have a contract - which is what the terms of service are - then if something goes wrong, asking a general question about "what are my rights" absent the entire contract is not going to get any sort of reliable answer.
Secondly, and again based on hard-won long experience with these things, it is rare that a contract question is answered by reading one clause in isolation. Here, for example, the contract relatively clearly (a) states they can pretty much do whatever they want and you have no recourse, and (b) defines auction and uses other language which can be used to decide when, under this contract, an auction is deemed concluded.
So, yes, I would agree with you that the contract clause which has been cited to you is inapplicable, because the auction had concluded at that point.
However, I disagree that you have a strong position or that engaging in the dispute procedure to which you agreed would be a good use of your time.