The Devil is in the details, and the details of a typical CAT analysis with the same content untagged in the TM will show a high fuzzy match, which will be minimally compensated with the all-too-popular discount schemes for matches that one often encounters. The reality, however, is that arranging these formatting tags can cost more time than actual translation.
The text analysis of Déjà Vu X from Atril includes a count of tags, so one could in cases like this use that information to charge the tags in some quantified way. However, most other tools do not offer such a capability, leaving us to consider the best approach to negotiating fair compensation for such a mess. Hourly charges come to mind in this particular case, though I seldom favor that for translation work.
It is a great convenience for end clients to work in complex, native or tagged formats, but it is important to recognize the extra effort this may involve, discuss this with the client and make appropriate arrangements. What approach have you taken to this problem in the past?