If you repack the zip file with a normal archiver, it doesn’t always work. Not quite sure, but I think you have to store it as uncompressed zip. Easiest way is to rename the original .mgc file to .zip, open it with 7zip, delete/add items, then save the file, and rename to .mgc – that works for me, at least.
And regarding the xml file: no, during the development process of pixel traps, there were some fundamental changes made that completely broke the profiles. If I launch one that still contains “old” pixel traps, Dosbox will crash completely. But it’s easy enough, just remove the code between the