I think I might have figured out the core issue.. so the helicopter entity is made up of several different entities, for the shadow, the rotor, the floodlights, and various other pieces that make up the helicopter entity we see.
In one of my previous updates with the base vehicle grid mod, I actually commented out all the lines I had for the helicopter, so no specific compatibility changes were being made. I also added the functionality that enables a default car grid to all vehicles that didn't already have a grid, and didn't have specific compatibility in place. This car grid must have applied to every single helicopter grid, and somehow became fully compatible.
For the customizer mod, I set the vehicle type to use an aircraft grid, but only applied it to the helicopter entities I thought mattered, but because it wasn't being applied to all of the other parts of the entity, there was somehow a mismatch of some sort, and broke the functionality.
I was able to fix the issue by just applying it to every part of the entity, should be working in v1.1.5