It's six of one and half a dozen of another :?
I have a Flowmaster 40 single in single out on my 2.8 V6 with 2.25" piping and everyone has seemed quite impressed with the sound.
Personally, after I've had the darned thing now for about 5 years, I wish I had just gone with a performance, but 'quiet' muffler if there is such a thing. I've found that while wheeling, the tone the muffler puts out gets a little bothersome and at Interstate speeds, the tone is a fairly high pitch that also gets a tad bothersome after awhile.
But at idle and medium speeds, I have to admit, the Flowmaster/exhaust setup I chose definitely makes the 2.8 growl a bit. Performance wise, it's probably a wash, but with the freeflow cat, larger pipes, and flipping the aircleaner lid, I was getting a tad over 400 miles to the tank. So, it 'seemed' the setup was a positive thing.
CKimbrough has a Flowmaster 40 with single inlet, dual outlet on his 3.2L Trooper and he seems 'mostly' pleased with it although he believes he took a performance hit with the larger pipes.
Strictly on what you've specified, the Flowmaster 40 will be just fine with the 3.1L, but I would upgrade the whole exhaust line.
Cheers,