I'd guess that yes, it does have the same problem with aftermarket knobs, because it does retain the same height as stock. I haven't actually tried putting an aftermarket knob on mine though, so this is just speculation.
i was thinking that being that its like a half inch lower that that may make up for that extra bit of shaft sticking out. hmmmm=.(.. i need it o work. im spose to be putting my shifter on this weekend too buuut i wont have the oppurtunity to test the other knobs for a little while. let me know what u find out.