@Kittykatluver16 Hello fellow cat (and Braver) lover I've yet to master the ins and outs of the bullet bow, but I may be able to help lay the groundwork for someone else to give a better answer.
Just to clarify,when you say you're using "the recommended skill trees" do you mean the in-game option which automatically allocates your skill points? And when you say your MEL power is higher/lower you're referring to your base damage stat as seen on the character info page, right? (Or do you mean your damage numbers that appear during combat?)
In any event, if it's not too much of a hassle could you recreate your trees here and share them with us? And maybe also share the difference in power numbers you're seeing just so we have a good sense of the facts on the ground?
In looking through the skill trees, I agree it's surprising that your MEL dmg would be higher with Ranger as a sub as it looks like only 1 skill on that would work with MEL (i.e. First Hit, but this should affect RNG the same way). And you're also correct that while Hunter's Fury Stance buffs both MEL and RNG, some nodes give a bigger boost to MEL so it's also surprising that RNG wins out in that class...
Sorry I can't give you a better answer, but we'll get to the bottom of this!