I doubt that FCP7 running under OSX 10.7 (Lion) will call files in another volume before locating them in its own volume. And what FCP7 library files would be "native" in El Capitan but not "native" in Lion? However, if FCP7 does do what the Apple rep fears, you can stop it. Most simply, you can unmount (or eject) the El Capitan volume whenever you run Lion. Or you can prevent your Lion volume just from accessing programs in the El Capitan volume. The nice, inexpensive TinkerTool System software automates these operations.
I doubt it's necessary, but to be absolutely sure your new FCP7 installation is completely in the Lion volume, unmount all other volumes when doing the install.
External vs. internal drive is not relevant. This is a volume-by-volume matter. Your El Capitan volume might have priority for booting, say after you reset PRAM, but it is not the center of your universe. You can sit in your El Capitan seat or your Lion seat, etc. That's the best thing about Macs, in my opinion.
Complications arise with hardware, that must run and might be incompatible with one or the other OSX, but for software you can decide which OSX suits it best. I found Lion to be the
last OSX fully compatible with FCP7.
Dennis Couzin
Berlin, Germany