Yes, that's my point - all trigger e-mails can be customized, so in current UI there is no clear way to resolve the problem. The problem is - there are many triggers and different subscribers, but some subscribers specified in several triggers and all triggers use base template (empty body, subject etc.), so if several triggers run in same time, user will receive several duplicate e-mails. And in current UI there is no way to prevent it.
The good way to fix this is - if trigger doesn't override any field (so it generates completely same e-mail as another trigger), then there should be only 1 such e-mail for specific subscriber. In more general case - we need to collapse generated e-mails by hash(body/subject/etc.) and then make recipient list unique by passing it in set.