I've not been told this, tbh a lot of the treatments, antibiotics, creams, soaps etc are probably more likely to damage your microbiome I would have thought. Is this a GP or a dermatologist? You need a dermatologist.
Tunnelling usually happens much later, years after symptoms first develop. If you press on one area another area will bulge because the fluid had moved.
Neither I or my brother are autistic, I was told it is genetic though so you should take your son to the doctor.
Covering them helps as it relieves some of the pain, stops them rubbing and you get less pressure. Magnesium sulphate paste can help draw them out and make them burst quicker which hel6with the pain. I have been prescribed hibiscrub to wash with and dalacin, which is actually a treatment for bacterial vaginosis, to put on under the dressings. I also have long term antibiotics. The combination of these things really help.
I don't think diet has ever helped, but losing weight did a little bit. My mother insists the homeopathic "doctor" she took me to, who put me on a wierd diet helped, but I'm more inclined to believe it was placebo, chronic conditions ebb and flow, you tend to try anything when it's at its worst so things can only get better.
Surgery did help and I am awaiting some more, but this is a drastic solution best left for if it gets really bad and persistent in the same area.
The best advice I can give is to keep on top of your mental health, it can get you down and make you feel shit, don't let it get you down.