There are no good reasons you don't see more turbo 4.6s. The pros: for a 4.6, you can run your stock block to much higher hp than 5.0s. Cons-worse stock rods and pistons compared to pre 93 5.0s. But pistons/rods are easier and cheaper than aftermarket 5.0 blocks. I think the other thing is a space issue. It is a little harder to run the pipes with the wider 4.6. That being said, someone on turbomustangs just ran everything under the crossmember and it really was not bad. If my procharger ever dies, my 97 will become a turbo car for sure.
97 Laser Red GT-248A Wingless model, Built Lincoln Mark VIII motor-Procharger D1SC, 3 core IC
2012 Black GT-Saddle, 3.73s, Brembos, Shaker1000