I haven't seen a definitive answer from APS, so it'd be useful to confirm with the editors directly. However, based on the agreement below there's no reason to think they would reject open access papers for that reason. They could, in principle, have some internal policy to that effect, but APS is generally quite permissive when it comes to preprints so I wouldn't expect them to. (Given that CC-BY even allows commercial redistribution after publication, it also doesn't make much sense to ban preprints just because they were posted before publication.)
When publishing under open access there's no need to transfer any copyrights. Instead, APS uses a shorter publication agreement that, in its entirety, reads
Subject to the acceptance of the [above-listed] Article for publication in a journal of the American Physical Society (APS), the Rights Holder(s), where applicable, or the Author(s) hereby agrees:
- To grant APS permission to publish the unpublished and original Article, the abstract forming part thereof, all associated supplemental material, and subsequent, if necessary, errata in a journal of APS under the Creative Commons Attribution 4.0 International license (CC BY 4.0), http://creativecommons.org/licenses/by/4.0/.
- That further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.
- That any subsequent Reply to a Comment accepted for publication in a journal of APS, for which this work is the target of the Comment, should also be published under the same Creative Commons license as this work.
By signing this Agreement, the Rights Holder(s), where applicable, or the Author(s) jointly and severally represent and warrant that the Article is original with the author(s) and does not infringe any copyright or violate any other right of any third parties. The signing person(s) also represents and warrants that they have the full power to enter into this Agreement and to make the grants contained herein.
Note that, unlike their usual copyright transfer agreement, there's no mention of preprints or copies on your website. However, since all you give them is the permission to publish the article (not the copyright to it), as far as I can tell posting the preprint under CC-BY should be fine.
For future papers it could also be worth using the standard arXiv license until you know where the paper will be published, and under what terms. The license can always be changed when the arXiv posting is updated.