Of course cubes matter, more cubes equal more torque production and a quicker powerband (comparative setups).
And TFSCoupe, there is a world of difference between a 281 DOHC and OHV 302. The heads are a small portion of that difference, never mind the flow numbers but velocity plays a huge part too. Aside from the difference being that the 302 is oversquare (bigger bore than stroke) and the 4.6 is square (similar bore and stroke), there are many factors that tell you which turbos will work best. As with everything, it comes down to combination combination combination. You cant expect the same turbo from a 302 to work the same way on a 281.
Getting back to the thread starters concerns, a large bore 347 will work great and I would personally rather run a large bore 347 than a smaller bore/larger stroke 347. It helps to keep piston speed down among other things. There are many benefits to going this route, and it will make awesome power with the right parts.
'86 GT T-Top - 5.0/T5 - in pieces.
'90 LX Vert - stock
'83 Cutlass Cruiser LS/LR4 swapped, TH350, 8.8 rear swap