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You can do what you like with the TM system. If you wish to modify your own site templates using the TM system, feel free. It's not the designed use of it. And you can't easily modify specific styles with the TM system.

The designed use of the TM system is for add-on developers to easily distribute changes to the default templates.

Since XenForo 1.2, there is a wonderful 3 way merge system, so it's no longer advised against to edit templates directly.

The bonuses of editing templates directly is that you can apply different edits to different styles. That's something you can't do with the TM system.

There isn't a reason you shouldn't use the TM system for the day-to-day edits you want to do if it works for you. But at the same time, there's absolutely no reason why you shouldn't just directly edit the templates, either.