As a hint about what makes the Renai Transportation thrower recipes special, I believe the thrower items are created in the final fixes pass, with thrower versions dynamically created for each inserter type. The Nullius thrower recipes are created in the initial data phase, but since the items don't exist, they create inserters as a placeholder. Then in final fixes their result is changed to point to the actual thrower item, now that it exists.
If GCKI is modifying the recipe, that could easily trip it up. Perhaps it's turning "result" into "results", so when result is later updated it has no effect.
But inserters aren't vehicles. GCKI could bypass having to worry about all these weird corner cases by just having a function that looks up if the recipe has anything to do with vehicles and not modifying it in any way if it doesn't.
I could add another workaround for thrower recipes, but I'm worried about other weird interactions with other mods that dynamically create recipes like Transport Drones, etc. It seems more appropriately fixed on the GCKI side to categorically not modify recipes that it clearly doesn't need to.
Note that you're getting a lot of reports from Nullius players, but I believe that's not because Nullius is particularly problematic here, but because GCKI is included in an official Nullius mod pack with around half as many downloads as GCKI, so naturally a lot of active GCKI users have it from that mod pack. But I suspect that over time reports will come in of similar issues with other mod combinations, not related to Nullius. So these issues are not all things that I can fix on the Nullius side.