Is it because JF BAe 146 product is available on both P3D and MSFS?
If the airplane has exactly the same name in MSFS and P3D, but has different physical dimensions and/or door placement and/or center of mass or anything else that would cause the distances in the airplane profile to not be compatible, then yes, that's surely the problem.
During testing, we didn't found any airplane made like this, usually developers change the airplane name in MSFS, and the ones that didn't ( Aerosoft CRJ and Leonardo MD ) was because the plane *was* fully compatible with the P3D dimensions-wise.
I'd say that if there are some planes out there with this issue, we'll likely have to add separate airplane configs which are only valid for one simulator. We assumed that, if airplane developers followed a standard of using the same name ONLY if the plane was compatible with both version was a sound one, because it would have prevented users to redo configs which were already working, so not isolating airplane configs like we already do for airport configs was made on purpose.