When you say, "I have the upgraded filter' do you mean a Uni or the CF Moto version of foam filter?
I agree that nothing gets past the spark plug seal and threads. The mechanic will have said that the plugs were that colour because that's all he saw. If he took the heads off I'll bet that the whole underside of head and top of piston was the same red shade. Wouldn't be JUST spark plugs alone with red clay dust.
The intake tract needs secure airtight fittings, proper foam filtration and that filter properly oiled with the right foam filter oil.
I keep being amazed at the number of people even in the business, who still don't understand how foam filters work and who still think it's fine to use K&N oil on them and tell their customers that 'advice', as one instance.