If I include a mod in a template's settings and that mod gets updated, will my template's settings continue to refer to the older version of the mod or will they be updated to use the newer version? (I.e., if I create a new game using that same template, which version of the mod will it use?)

Edited 4/11/2017 02:21:51

It will always point at the latest version. Therefore, you need to either:
A: Make your mod backwards compatible with everything you put into Mod.Settings
B: Make a new mod when you change stuff, and un-mark the old one as public.

Would it be possible to target a specific release/tag on GitHub for mods?