At Planimeter, back when we were "Team Sandbox," we ran into similar issues when attempting to publish Half-Life 2: Sandbox.[1] People can still find the source and game code on our repository listings from when we migrated off Google Code.
Valve Business Development did not give us the go-ahead.
Notably, we were the first usage of LuaJIT in the Source Engine, and we think that later GMod caught up to us. But you couldn't use native Lua modules prior to then. Only with our mod.
Half-Life: Update failed for the same reasons we did, and also our team was in our 20s when we were about ready to publish, too.