What are the expected future uses of the dot?

None from me, but see below.

Another approach would be to just remove the warning and allow either dotted or un-dotted extensions to be used, since it's extremely unlikely anyone will intentionally be wanting to handle plugin files in Geany's plugin dir like theplugin..so.

Yes, that would be a valid fix from my POV. I don't really like the current state because it emits a warning only for something that is very easy to fix; so it's easy to forget, while easy to fix. This way, it's likely authors might just not see/ignore the warning because it has absolutely no side effect, and then the dot prefix effectively becomes a part of the API.
So, IMO it should be either allowed or disallowed, not transparently "fixed" yet not officially allowing it.

BTW, even with stripping the leading dot unconditionally, someone could very well support ..so extensions by simply pass ..so as the extension: one dot is stripped, the other stays, and voila.
Well, actually it would require changing how the extension matching is implemented to merely do str_has_suffix() otherwise the dot will not be considered, but still.

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