I've seen a couple of different compressor configurations. The one that you've described on the carb side with the battery in the boot and another on the exhaust side where the battery stays in the engine bay. Not sure if they changed at some point but they were made up of parts from a couple of different Ford models so it could have been what was on the shelf at the time.
I bought an engine from a TE Cortina a while back with the compressor on the exhaust side, clears my Genie extractors but in the Escort it clashes (only just) with the brake booster. Eventually I'm going to use that one and move the mounts back by a few millimetres, one of those when I get around to it jobs.
I would have thought the compressor would clear the 45's they don't hang too much if any lower than the original manifold.
Out of interest you can still but the compressors new if you want to go down the originality route.
Cheers Drew