I propose that when standard inputs are set up as an AUX input because S1-5 configures them that way to input the audio of an External Instrument, the FAT channel is accessible on that AUX channel.
With the new External Instruments feature, the audio input channel appears as an Aux channel, but there is no option to use the FAT channel plug ins from the input channel (I'm using a StudioLive 32R for all the inputs)
If I set up a regular input channel for an instrument, I have access to the FAT channel and can adjust the parameters. But for an External Instrument, it's the same input channel, but it shows up as an AUX IN channel and the FAT channel is missing (See Photo showing the same input set up as regular input and External Instrument)
Input channel set up as a normal input for capturing the synth:
Exact same input from the Mixer/Interface, but set up as an External Instrument AUX input: