As I understand it, in AtoM's data model, an Archival institution is simply a special type of actor, which is the internal data model name used for entities described by authority records. We can see this in the early (and incomplete) entity type diagram still found in the documentation
This comes from the very earliest days of AtoM's development, and has been carried forward since. I can't personally speak to the rationale for modeling the entities like this, rather than making an repository its own kind of entity.
I do personally think that even if this is the case, it's a usability / user inteface bug that one can find and select archival institutions from the drop-down menus for linking authority records. This seems doubly so now that we have a separate field for linking an authority to a repository record, something that didn't exist prior to 2.4.
I found an old ticket where it looks like this was raised, and was causing errors. Without having had a chance to ask for some more history internally (I'm traveling for work at the moment, with intermittent email access), it seems that removing repository records from the autocompletes may have been more complicated than originally predicted, so they settled on simply fixing the 404 error and verified the issue. See:
Despite this, we do now have a more consistent way to link authority records to repository records, for those who wish to do so. I personally agree that this is confusing for end users, and ideally we should prevent repository records from showing up in authority record autocomplete fields. To that end, I've filed a bug ticket to track this fix request:
As ever, I can't guarantee a fix for this will be included in an upcoming release without community sponsorship, but I have added it to our internal list of community-reported bugs for us to track and try to address for 2.5. Whether we are able to or not might depend on what other critical fixes come up, and how complex this turns out to be once we examine it more closely. There may also be further backstory about the rationale for this, of which I'm not currently aware. If I learn more that would be helpful to share, I will do so here.