Interesting; in testing, the "Game finished" dialogue still appeared for me, but I don't test for achievements, so I can't comment on that.
I do see that the core game silo-script.lua seems to have been updated to v2 at some point, and I haven't updated the mod's interface with it since v1. However, it does not seem this would cause any problems unless you have an old savegame that was created in an old Factorio version that was running v1 of the silo-script (or from before silo-script was split to its own file). Were you testing using a savegame originally created in, say, Factorio 0.15.X? If so, then I can understand why things are not functioning as intended.
Do note that achievements earned while mods are active are counted separately from vanilla achievements anyway, and I believe they won't be synced with the list of completed Steam achievements.