Would a Federation warship like the Defiant out gun a Star Wars Star Destroyer? Who has a bigger armada? Who has the tactical advantage? Don’t forget that The Federation includes the Klingons, who love warfare and have fast, agile, heavily armed ships, with cloaking devices, and the Vulcans with superior logic and tactical planning.
Transporters block shields regardless of modulation. You can modulate weapons to penetrate shields, but transporters are trickier. “We can’t get the away team back because shields are up!” would be a non-issue if the shields could be modulated to block weapon fire but allow transporters.