I don’t play a hunter and you gotta go with what works for you but I would think that once you MD you should go all out to transfer as much threat as possible. Then when that temporary threat decays you should have blown your cooldowns and are pulling less threat. Once Vengance stacks up a decent tank should be able to hold you off even if you outgear them. After all they have a 3x threat modifier plus you are out of melee range so the mobs won’t turn on you until you are doing 110% of the tank’s threat.
From that it sounds like you aren’t having difficulty in a regular raid but with different tanks, presumably mostly in randoms. If so I wouldn’t rule out outgearing and bad tanking. A lot of random people just aren’t that good so if you are cutting edge DPS you’ll have to adjust. And I see a lot of tanks still in the WotLK mindset and gimping their avoidance and threat by stacking Stam.