My mistake, but what I meant to articulate through my question was: is there a way to disable that feature in STP?
Your method works, yes, but you can see the obvious downside in efficiency. In regard to panning, it's a similar problem, in that I have to make edits twice (in some cases), add effects twice, etc.
One would assume that if I link the bloody files in FCP, I **** well went them to stay that way...
While you like to think of the two files, once linked in FCP as a stereo pair, you captured dual mono and that is what the material is. FCP is a non-destructive editior. It will not change the original files - and that is what STP reads.
The other way around this is to take the file offline in FCP then recapture it using the correct audio setting (stereo).