I think you are forgetting the context of this post, which is non-destructive testing. Obviously you can do a lot more with destructive testing, but then that would be a different topic. I'm guessing that's why you are under the impression that I'm not understanding you.So you have no baseline control to compare to. Sloppy test methodology and won't give any real good comparison if you're just comparing bad ones to bad ones. The "best one" you test may still be way worse than a 100% "good one" baseline. Baselines exist in testing for a reason. Don't know why you can't seem to grasp that you need a known "good one" baseline to make any real sense in the testing.
What is being compared is the pressure differential across the filter media and bypass. The idea is that this restriction will be lessened (and therefore the differential lowered) if there are leaks. We can assess the difference in pressure differential at different flow rates, and the chart will look something like below. As you can see, at higher flow rates, the difference between the two pressure differentials is larger, which will be easier to detect. Adding more restriction elsewhere will reduce flow rates, and make the difference harder to detect.You wouldn't want to choke it down too far which may do what you described, so maybe block half the inlet holes. I think with the vacuum level higher inside the filter, if the leak gap around the media is present then it would effect the level of vacuum more on the guage compared to if the vacuum level was at a very low level to start with. So essentially making your vacuum gauge more sensitive to a gap leak path. Try it and see if you're going to play around with this "science project".
Yes, the air is at ATM pressure before it flows into the base holes - doesn't matter after the air flows into the inlet holes. So that will be a constant (as well as the ATM air temperature) if you did comparative testing withing a short time frame. In other words, not one filter tested today and the other tested a week from now when the ATM pressure & temp may be slightly different due to weather conditions.
The air between the inlet holes and the filter media/bypass will be a bit below atmospheric pressure due to the restriction created by the inlet holes, which is what is relevant for testing the filter media and bypass. It doesn't matter much for comparative testing, but it's worth mentioning for accuracy.