I'm sure you could find a way to lift the shells of you 3 pending locos if that happens. Or you could just run them without the shells seated properly.
I'm just dumbfounded that you would be disappointed if they fixed them to be more accurate. I understand that you want them to match, but they do sit at the wrong height.
Either way, IM seems to prefer their locos sit too high
, so I doubt this will a problem for you.