I've only ever played with the modems with the over the air baud rates matching the APM baud rate. Though saying that i've run into a few problems myself with low % telemetry (X-tend) whilst airborne. Everything ground tests fine but airborne we're getting quite a lot of drop-outs. Unfortunately I have quite a chain of devices for telemetry at the PC end. Usb--->serial converter---->serial to TTL converter---->digi x-tend so you can see I have a bit of work to do to find out what's causing the problem!
I thought you had to match over the air baud rate with autopilot baud or there would be lost data/lag but i am a bit of an amatuer TBH.