I wasn't envisioning this change actually occurring FDR, but hypothetically through the config templates was where I envisioned modes being specified.
Examples:
Foo.ini "For standard airplane control surfaces (Mode 1)"
Flibber.ini "For elevon airplane control surfaces, (Mode 2)"
I imagined that if a desirable config existed already in say mode 1, and somebody wanted it for a mode 2 setup, they'd probably make the changes and publish that for others.
The differences aren't great, and even in a really complex config it's usually possible to do a find and replace in an editor pretty quickly -- or it would be if there weren't ambiguous tags any more.