I believe it was built this way because it was designed to be a reverb pedal, but so many requests were made for them to make it also able to load cab/mic IRs that they came up with the firmware to make it work.

I've had no trouble with it in the loop, but I'll have to try it using the main outs to see if there are any issues. I think there is enough control in the output of the 11R to make it a non-issue though.