AFAIK Calibre does not reorder the tags in the database - but in some places it presents them in sorted alphabetically - eg the book list, book details, the order they're held in the database is shown in single metadata edit. See ==>>
Sorting tags into specific order
I don't know what order they're presented in the template language list functions - I would guess order entered, but chaley would probably be the best person to ask - I'll give him a nudge.
BR