d20 Modern uses a lowered massive damage threshold (Con score instead of 50), class Defense Bonii, and 3.0-esque feats. Making the two "seamless" would involve including or disincluding these from one or the other to match the disparate elements.

That said, in a "who wins, Modern or Fantasy" match, I'd have to put my dice on the Modern crew for levels lower than 6 despite the poor performance of firearms. Around 6, things get a little funky and it's more likely from that point forward that things will go to the Fantasy crew. This is due to the existence of Tear Gas and Stun Guns. The former is a DC 25 fort save or choke for 2d4 rounds (and keep saving each round you're in it, disperses after a minute) while the latter is a melee touch attack for d4 electricity damage and a DC 15 fort save or be paralyzed (until you're Coup d'Grace'd next round).

d20 Modern has a flatter power curve than D&D, you start out meh, get decent, and stay decent. Mostly this is due to the fast scaling defense and low massive damage threshold. Tear Gas remains terrifying up to about lv 15 in d20 Modern, tho. Stupid Tear Gas...