Well... managing a single project with many developers all around the world is a challenging task indeed. As far as I know in such situations all work on their tagged builds, and a good commits gets occasionally merged with the dev branch... but it still requires extensive testing after the merge and is human error prone.
To be honest the problems with the current official build were the reason I came here crying for help quite soon after my first tries so it was kinda good

Skipping the default.ini will not be good... a "new" version could be detected by either datestamp (sigh) or some filename format. I can't count on the first way to be stable. The second looks more promising and best of it, does not rely on human to edit some file to let the people know.
a structure as follows:
scp/downloads
--fs2_open3.6.6.zip
--fs2_open3.6.6.txt
...
--mv_core1.0.2.zip
--mv_core1.0.2.txt
--mv_models1.3.5.zip
--mv_models1.3.5.txt
This may do work for the default.ini-less updates. The launcher looks in there and compares. The text files are the changelog in fact, the launcher should update only files present in the system i.e. although a new mv_cell file is out, if the user does not use the cartoonish textures, no need to download them. I refer "zip" as a general compression, 7z can be used for example too since it offers better compression than even winrar, + it is free and + I think it offered a small decompression prg/lib, just ideally suited for the purpose.
This if the launcher downloads and extract the files by itself. The other way is a simple nsi script that finds the freespace2 folder and updates the file, while the downloading is left to the user - best compression, automatic install.
The drawback - linux users will not be able to run the exe.