It's OK. But you have 2 possible additional solutions (random order, without ordering on convenience and efficiency)
- Perform additional merge(s) before (full-range) main code merge: merge config files only with
--accept 'mine-conflict'
(ignore branch-changes in configs) - Merge (full range again) with
--diff3-cmd SOMETOOL
, where SOMETOOL is specially created tool, which will ignore all changes in config-files only