It's an intended bug, feature, change, ect.
I should not adding the train-layer a second time to any entity. I should only be adding the train-layer collision mask to the other entities. I should have all entities that have the train-layer by default black listed from my mod's function of adding the train-layer collision mask.
I'm not trying to be rude, but as far as I know there is no way to fix your issue with out changing how my mod functions which sadly would only cause more problems then just the one issue you've run into. That is why I made the change I did with how hovercraft collision is handled compared to the original mod. Even the Wube devs complained about how that mod was handling the hovercraft collision/hovering. I honestly wish there was something I could do for you because I want you to be able to enjoy my mod; however, as far as I know there isn't. I am open to suggestion and very much appreciate your input.