Hello!
What data type are you working with? I assume EEG?
In MNE, I’d suggest to add bad channels to info['bads'] and not interpolating until you really need to. This is of course to some extent a personal preference, but in my experience, interpolation is only really needed when you want to calculate e.g. a grand average and need to ensure all participants have the same set of channels.
You should not set the average reference before running ICA. I’ve seen cases where this would “smear” artifacts across all channels. So my advice is to first try to remove all artifacts (which includes use of ICA), and only after that switch to an average reference.
MNE is aware of the fact that some channels contain brain data (e.g., magnetometers, gradiometers, EEG) while others don’t (e.g., EOG, ECG) and will take this into consideration. Applying an average reference to EEG data, for example, will of course not include EOG channels in this calculation.
I hope this helped a bit!
Richard