There's no way to set timing methods per-category or per-subcategory. However, what you can do is make sure "Show empty time columns" is unchecked, and manually enforce the timing methods you want to use on each run.

Yeah my game (Battle For Dream Island Again 5b) has this issue too where we use RTA in one category then IGT for others. All you can do is make one of the timing fields empty for every run so they sort right.