I think it's better to fill the filter up before installing it - but to your main issue, if you put in the correct amount of oil (and assuming there are no changes that would change that amount like, for example, a different oil pan), I would trust your measurement over the dipstick. Assuming your dipstick is seated in a repeatable place, I would mark your stick to show the actual full mark. Something else that is important, but I'm not sure how you would test this, is that the crank not swing into your oil. You'll lose power and froth up your oil making it less effective.