Martial Dominance has a prerequisite of 1 rank in intimidate. So, if you get all the ranks back you no longer qualify for the feat. Versatile Training states you retrain all the skill ranks. So, obviously using the rules for versatile training would invalidate the feat.
The other thing to consider is that other feats may require specific ranks in intimidate, if you retrain those ranks you no longer qualify for those feats.
I remember a James Jacobs post where he wishes they’d have included the language for retraining earlier. I’d call it an officially recommended house rule to allow retraining with those kinds of options.
https://www.enworld.org/threads/bard-versatile-performance.270621/
Versatile Performance's design goal was to give bards more skill points without artificially increasing their total skill points AND to put an emphasis onto the Perform skill for them after the Perform skill's importance regarding bardic performance lessened from its importance in 3.5's version.
The result isn't perfect, alas. And it's something that I very much would like to see addressed in FAQs or errata or, most likely, in the upcoming Advanced Player's Guide.
The two basic elements: bards should be able to "reschedule" their skill ranks in skills that Versatile Performance duplicates every time the gain a new Versatile Performance; this allows a bard to be good at, say, Fly and Acrobatics until he gets Versatile Performance (dance), and once he DOES get that, lets him reapply skill points previously spent on Fly and Acrobatics to other skills. This'd work similarly to how sorcerers get to repick spells periodically.
The other element is that when you use Versatile Performance to use a Perform skill for another skill, bonuses you'd get to that other skill from things like Skill Focus or other Feats, racial modifiers, magic items, and the like SHOULD apply to your Perform skill check when you're using it for those particular versatile skills. In effect, Versatile Performance gives you a pair of "phantom skills" with the corresponding "phantom skill points" each time you gain it.
If instead you want to just kill the Versatile Performance ability entirely, my suggested fix would be instead to increase the base skill ranks per level granted to bards by 2 each time they would normally gain Versatile Performance. These skill rank increases should probably be retroactive.
ANYway. It's something that I might call a personal crusade to get fixed. Might be a while before it sees print, but them's my thoughts, anyway.
It is possible the design team ultimately decided that their upcoming skill retraining system was enough to address this issue. But at the least, allowing it for free is a designer recommended house rule. Maybe that will be enough for your GM, if not you can hopefully use regular retraining.