My experience in these matters is that ANY change to the gear and the location of its parts would void any specific warranty. But we all know that when it comes to combo switch gear, the locations of pt's, ct's low voltage wireways, etc....leave something to be desired. At our company, we make the manufacturer aware of the problem, ask for advice, or what we can change ( in writing), and if they don't budge, we make the changes anyways. As long as the changes do not violate the nec, and DO provide a safer way or more practical way ( which many times means a safer way), we change it. Too a point of course
But in regards to the ct's and there locations, the ct's are "listed", but this has NOTHING to do with they're location. I could show you numerous examples of this.

I'd say you did the best with the situation, and made the right choice. Its the kind of things that must be done in the REAL world.
( Don't even get me started about working 480v hot)

Regards
NS4M