Fix config merge order, add test

[neko-kai]

Config merge order was reversed (common was higher application, *-reference was higher than regular)

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 66.33%. Comparing base (ee07a39) to head (3fa939a).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #2161 +/- ## =========================================== - Coverage 66.50% 66.33% -0.17% =========================================== Files 589 581 -8 Lines 11446 11399 -47 Branches 1255 1250 -5 =========================================== - Hits 7612 7562 -50 - Misses 3834 3837 +3 ```