This is a problem currently, yes. We don’t support building with modified versions of the SDK or NDK, and there are a few apps that require one or the other (the latter is more common). There are plans to support this in the future though.
I am currently tagging all releases published with Google play (last one is r33). Additionnally, I would like to make alpha releases available through F-Droid, if they are clearly marked as such in the f-droid interface.
If you want to use alpha releases, we would need to change Update Check Mode to none and set the current version manually. Then , you can post the commit etc here, or do a merge request on gitorious.org. Otherwise auto update is possible but risky as , if something breaks, our build server doesnt give us much feedback.
The F-droid client puts an asterisk next to one build, that whose version code is equal to or closest to the Current Version Code as taken from the metadata. The Current Version Code can be automatically updated or manually updated, depending on the app.
You provide a Build Version line for 1.6.0a1 but you leave the Current Version (Code) unchanged. That way people won’t be prompted to update. The Current Version is only updated for stable releases which can be done automatically by checking for new tags. You can provide Build Version lines or Current Version changes via git or via the forum.