Depends....
If the output levels from the RCA and XLR are not matched (and they're usually not - typically +6dB from balanced XLR compared to unbalanced RCA), and if there is no way to correct this with gain controls on the amp, then one section of your speaker is going to 6dB out of balance compared to the other.
In the case of carlthecat's example, it could be that the difference heard is because the highs are as much as 6dB in elevated signal level above the lows. If you like the sound, fine, but I'm just saying...
Also, for the record, biamping with 2x200 wpc is not anywhere close to the power equivalent of 400wpc amp driving the same speaker.