Consider using interdiff for comparing two merge request versions
Let's say we want to see how Version 2 is different from Version 1, while excluding fact that Version 2 has merge from master .
This can be done by comparing Version 2 patch and Version 1 patch with tool like interdiff
# Version 1
git format-patch fbe54b07..ffd3fa22 --stdout
# Version 2 (rebase from master)
git format-patch 88a72101..91d152de --stdout
# Diff between version 1 and version 2:
interdiff <(git format-patch fbe54b07..ffd3fa22 --stdout) <(git format-patch 88a72101..91d152de --stdout)