So I just did the TL gear change this summer and if I remember correctly the gears didnt line up perfectly for me as well. For what its worth, Ive had it put back together for weeks and been riding it and I haven't noticed and troubles or funny noises with it.

For those maybe interested in the future.  I sourced a newer cover.  Here is a case comparison side by side.  The TL boss is 1/2" down, and the inside hole is also drilled down to the same depth as before.  I'm not convinced the old case could be modified without coming through the other side... but apparently it's been done?  You can see the additional metal inside and outside.