config.h: Align the divergence between mldsa-native and mlkem-native in config.h

[willieyz]

• During PR #686, we found several divergences between mldsa-native and mlkem-native in config.h.
• For example, in mlkem-native, MLK_CONFIG_FILE is the second entry, but in mldsa-native, MLD_CONFIG_FILE has been moved to the fifth position, mixed with the native backend–related configuration macros. If we align these differences, it will make further porting or modifications much easier and help avoid issues like the missing macros fixed in PR #686.