After doing some more testing, I've confirmed where the problem is
The weapon needs to be allowed in the team loadout in fred. If its not, the thrusters just won't show up.
This is not really ideal, since in general you'd don't want the subtituted weapon to be visible to the player in weapon loadout menu
Hmm, well that makes sense, the engine is not loading something that "can't be used". It would probably also work if you equip the substituted weapon to an AI ship that is not involved in the fight at all.
However, I will take a look because this feature should just work and not require any weird work arounds.
EDIT: I may have found the issue. Please try the following build. If the problem remains, please run the build with the attached debug_filter.cfg.txt (save it as debug_filter.cfg into your root data folder (same place you find the log)) and post the resulting log after you run a mission with where the problem appears.
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