I retired in 2001, so have no recent experience. I suppose that the GE guys "tweak" the software also. I do know that at the time GE developed slow speed/flood loading control for the AC4400's, they tested with multiple GE AC's and also with DC units. In addition, they tested on various railroads in actual flood loading service. I assume but cannot confirm that GE tested mixed GE and EMD consists.
There were no "unusual situations" seen during this testing such as "wheel chatter". I have no recent knowledge re the performance of AC units on NS.