I also have the Power supply anti-glare screen.
It cuts down dramatically on fingerprints and fingerprint smearing that occurs from normal use. Also you can tell that it reduces glare, you can no longer use the ipad as a sort of mirror.
However i have to say i can definitely tell that the screen is sort of blurrier, its sort of looks like there's a layer of blurry pixelation between the screen and me. I noticed this very shortly after putting the screen on.
I'm considering switching to a non-antiglare screen because of that. Mayo7 (or anyone!) can you confirm that the screen still looks excellent with the Power supply clear film?
Onto your actual question,
I just borrowed a pogo sketch from a coworker (who also has an ipad), he did say he wasn't crazy about the pogo, and told me how he lost it in the couch for a week and forgot about it...
I used the pogo with a free "Draw Free" app, drawing out "Hello world" with my finger vs the pogo, drawing the the pogo is fast and easy, I can actually draw hello world faster than i can "draw" hello world with my finger.
I switched over to safari and used the stylus to "type" in a web address, the software keyboard picked up the pogo's "typing" with ease.
I have noticed though that when i hold the pogo at an angle to the ipad (like i would if i was holding a pencil) such that a small amount of the tip is against the screen that occasionally the ipad will miss a small motion i make with the stylus.
For example in safari if i i try to use the pogo to "flick" the page up or down (to move up or down) if i do a small flick (moving only about half an inch) with the pogo at this angle that the ipad misses this motion.
Honestly i think the same thing would happen if you didn't have the screen protector.
So from using the stylus with the power supply antiglare screen for about 30 minutes i'd say the screen does not affect the stylus operation. I haven't tested the stylus without the screen protector so i can't provide a comparison.
Hope this was helpful to you