I can't tell about all cases but in short problems happens when u use SDK building and u already understand it. For PC version it could be simply avoided to not using SDK building (yeah, I know that there are possibility to inherit infection if original game has virus but anyway UAGC have some features to prevent most of 'em) but here we go to MacOS where u can probably avoid SDK building too by injecting compressed files inside game original zip but with high risk of getting permision errors later.
So for now I don't think there are anything I can do about it and problem and from my opinion it's not connected anyhow to UAGC. I can only sugest don't forget about game run test after compression.
For those who interested in more detailed explanation here is 2 cases of fonts problem that I've analyzed:
Case 1: Here dev modified SDK by putting some custom font "Yipes.ttf" inside "../renpy/common/" and when u build it with original SDK font wouldn't be copied because it doesn't exist there.
Case 2: is more comlicated and I'm not 100% sure is it dev fault (maybe not intentional) but after I've decompiled options.rpyc file that tells SDK what files would be added to rpa and what rpa SDK should create I found out that there are should be line called something like "build.archive("others", "all")" because without it others.rpa that contains fonts and some other needed files wouldn't be created. I've even can't build game with SDK until deleted some folders with language files and even after fixing the problem game files system wasn't the same if compare compressed + SDK build vs original (some files and folder remain unpacked). Probably in this case "pack back to rpa" feature should solve the problem but since u do SDK building anyway sometimes it's glitchy (SDK makes *.rpa.rpa files if u feed it some rpa files so u need to pay attention).