From the pictures I've seen of it, the Pro Flo ECU and harness appears similar to the Holley EFI stuff. I can't see how you'd want the entire harness in the engine bay if it's even possible. I have a Holley Terminator X and mocking it up I learned pretty quick there is not a lot of room to mount an aftermarket ECU and harness under an E body dash easily and/or cleanly. This is especially true with an A/C heater box.
I thought about putting the ECU under the driver seat or the console. The seats are really low in these cars though and figuring out how to route the wiring out from that area would be difficult. Not sure if there would be enough room under the console, might be worth a look. Or, if you don't care about it being out in the open it could be mounted in the passenger side foot well like a race car wiring/ignition panel. I don't think there's enough room behind the kick panels.
Right now I'm looking at mounting the Holley ECU behind the rear seat or in the forward part of the trunk and running the harness up to the front in the driver's side wiring trough. I spent the extra coin on an unterminated, 15' "flying lead" wiring harness because I learned from two previous Holley EFI installs the supplied harness is useless. My Challenger is completely apart right now though so it's easy to mock that up but it would certainly be a much more difficult prospect with the interior still in.
If you don't like the provided sleeving you can always discard it and use the kind you prefer. I like the split loom style and use non-adhesive tape and/or zip ties to keep it closed. You can get it in bulk from most of the electrical supply places.
In regards to the firewall - at some point you'll need to get whatever wiring is necessary into the engine bay. At a minimum you'd have to de-pin the connectors to even be able to route the wiring through smaller holes or cut it and use bulkhead connectors to pass them through. Maybe you can separate things into sub harnesses so you can pass smaller bundles through a couple different points.
Sometimes you gotta make stuff work.