I assume you are talking about for a GEN3 Hemi install? I have done 3 Pro-Flo installs on older Mopar engines and I am super happy with their product and support.. If I do a GEN3 swap, I will use Edelbrock for sure.
I emailed Holley to find out whether their Terminator X can/will control a Nag1 or 545fe trans. They have a harness for the 46re already. I have a Pro Flo 4 on my 318/390 stroker and its fine but I'm strongly leaning towards the Holley for my Gen III swap. I don't know if a transmission controller is in Pro Flo 4+ future. Terminator X Max is on sale until tomorrow night but backordered. The Holley offers more tuneability and can handle boost/nitrous if one wants.