In regards to intakes, I'd mark in black also this, because it's spatially separated from the fuselage behind.
And, actually, that part of refuelling probe that's not making one surface with fuselage behind it, also MUST be outlined in black.
In regards to the difference of opinion and being firmly on the side... You're pushing the red button...
I don't want it to sound too harsh, but if You think that established rules/standards/practices are outdated, then... it's not North Korea, You're not forcibly held here...
This is the official Shipbucket Style Guide & Standards Manual:
http://shipbucket.com/styleguide
There are some subtle differences between SB as written there, and FD as practiced, but the general idea is the same.
You ask: "should everyone be handicapped by the same outdated stylistic rules?"
My answer is "yes" - because that's what makes the SB style.