I have yet to see one of those checkers that worked properly. You have the correct length pushrod when, at exactly mif lift, your rocker c/l is at 90* to the valve stem. The c/l of the rocker is the line that goes through the center of the trunion and the center of the roller tip. When this line is at 90* to the valve stem, at mid lift, you're there. Weather or not you're on the center of the valve tip has nothing to do with proper pudhrod length.
As far as checking for proper pushrod length, it's the last thing I do when building a motor, and they're the last thing I buy. You should have all of your final machining done, especially the decks. Heads need to be final surfaced, valve jobbed, valve to deck distances need to be correct, cam and lifters, etc. Valve lengths need to be checked, as well...that is, if you're going to this extent. If not, just be sure you're confident you've done all the machining you're going to do. Obviously, the more HP you're going after, and the more sophisticated your motor is, the more important all the details are.
I'll use an old compresed head gasket the same thickness as the one I'm going to use, and install the heads, cam, #1 lifters, and upper timing gear. (the upper gear makes it easier to turn the cam, and keep it in place) I'll have no. 1 intake and exhaust valve installed, the guide plate and studs, (or shaft assy w/ #1 rockers ready to install) You don't need the crank in place for this. I'll have assembled the heads with #1 int and ex valves and light springs, and set a dial indicator on the retainer for the valve I'm checking. Make sure the indicator stem is parallel with the valve, not on an angle. This will insure a more accurate reading. Then I install the checking pushrod and rocker. I've made a taller, knurled adjuster nut for the rocker so it's easier to adjust. Then after setting the lash as I normally would, I run the cam through a cycle, recording the actual lift at the valve, then divide that number in half. Once I've done that, I'll again rotate the cam untill I get to that mid lift number, and look at the relationship between the rocker and valve. I get my face down real close to the head, and from the side of the rocker, I hold up a 2"X3" machinist's square, and I align the long edge with the centers of the roller tip, and the trunion. (There's usually a machining mark where the ends of those pieces are parted off, making it easy to find the exact center.) Then I'll move the square untill I have the short edge lined up visually with the edge of the valve stem. It takes a little patience, and a little dexterity, but you can see very accurately weather or not the line that passes through the two points on the rocker is at 90* to the valve stem, which is what you're looking for. I simply adjust the pushrod untill I get what I'm looking for. If you lengthen the pushrod, you'll have to loosen the rocker adjusting nut in order to keep the same lift number. If you shorten the pushrod, you'll have to tighten the adjuster. The important thing, is to always check to make sure you're still at that mid lift number when checking for square. The proceedure for shaft rockers is a little different since there's no adjuster on the fulcrum, and no stud. You use shims instead.
When I get the desired geometry, I rotate teh cam several times, looking at everything in operation. If I'm satisfied, then I remove the pushrod, and measure it.
I have, in the past, assembled the heads with the springs that I was going to run, and checked the geometry after the fact, and found no real difference. Besides, you're still only checking a static condition, and aren't going to be able to duplicate running flexation and deflections, so now I just accept what I come up with the checking springs. I know some guys that will add .010" just to anticipate the loads. I try and get the pushrods within .010" of the measured checker if I can.
Also, the other end of the rocker is as important as the tip, and needs to be checked, as well, for the same reasons. At that same mid lift point, the pushrod should be at 90* to the portion of the rocker that the pushrod cup is in. There isn't a lot you can do about this one if it's wrong, though, except to try another rocker. Watch the relationship between the pushrod and rocker as you cycle the cam, and see what's going on there. Look for excessive angle, interfearance, etc. There are a lot of aftermarket, import POS rockers out there that aren't designed, they're just reverse engineered off an existing rocker, and they don't quite get the details correct, which can be problematic, at best. IMO, rockers aren't a place to "budget" your spending, and you usually get what you pay for. Even the "brand name" rockers have their issues. It's just best to check everything.
Hope this helps.
That about sums it up!..
Key words: "It's just best to check everything"