We use playtomic all the time, Kongregate doesn't mind. Some other portals are really anal about it, but Kong+Newgrounds don't care, and I'm pretty sure Armor games doesn't either.
Armor was the ONLY one in my experience who has ever asked for tracking to be stripped out. I have no idea why though.
Most flash games use www.playtomic.com
for tracking stats and most major portals doesn't have problems with it
I dunno about most. swfstats/playtomic is better and definitely has the most presence on sites like FGL for obvious reasons but mochibot hasn't gone anywhere.
But yeah, I thought the question was about whether they'd care about you using your own home-rolled stats tracker or whatever as opposed to playtomic/mochi, which is a more specific question than whether they mind tracking at all. Right?