I've confirmed that if I use the lane editor to route a junction in the editor it does get saved and pasted in-game, but not knowing much about how that feature works exactly I don't know if the lane settings are firmly baked into the interchange in a way that will work even without the mod or if it is required in order to use the overridden lane rules.

A friend of mine's been playing the game and he doesn't share my Special Interest(TM) of optimising interchanges forever so I thought about making some prefabs for him but without TM:PE some of them will have serious merging issues.