Intake manifold painting

It depends on how good a job you want. I suspect if you don’t remove the intake, in a few months or a year, the red paint will be flaking off and, if it bothers you enough, you’ll then remove it and start over. Given the yellowing of the clear is bothering you, I think the flaking of the red will bother you soon too.

Sometimes one thinks the simple/quick job/effort will be good enough. Almost all of the time, it will look like a good enough type of job/effort.