No, they are different. The Flows are chambered mufflers, the Magnaflows are not, being a straight through with bi-directional baffles. Take a look at both of the websites.
The 44's have a different resonance which may help inside the cabin. They are still a 2 chamber muffler as is the 40 series. The 50 series then steps up to a 3 chamber design which will change the resonance and decibel level.
The Magnaflow is pretty nice...quiet burble at idle, nice when cruising down the road, a sound that gets people lookin' when ya get on it.
I've been running true dual Magnaflows on my SRT since 2007 and still like the sound. I've had the Magnaflow single in / dual out unit on my truck since early 2010.
I heard a Charger 5.7L with the Series 44's on it and it sounded good from the outside. Inside, it was a bit noisy for my tastes but then again, what doesn't sound good to me may sound good to you. I felt it was interfering with the tunes and I doooo like my tunes.
Good luck with your upgrade!