Again, my experience is with the P-09, not the P-07, so it's not apples to apples comparison.
Muzzle Flip: I don't know. I wouldn't be surprised if the PX4 was slightly less flippy.
Accuracy. I'm sure they're very similar, but the CZ's longer sight radius might make that accuracy easier to achieve with iron sights. If you discount called flyers, I'm keeping rounds inside of 3" freestyle slow fire at 25 yards with my P-09 with an RM07. I wouldn't be surprised if my examples were capable of 1.5" in the hands of a better shooter. I'd love to shoot an RMR'd PX4 for a comparison.
Sight Options. RDS is simpler to mount to the CZ. I really dig Langdon's Ameriglo sights for defensive use of the PX4. I don't think they're available for the CZ. Beyond that, both have a fairly limited selection.
The CZ is available with a threaded barrel, if that matters.
Ergos. The CZ fits MY big hands better. The P-09's beavertail prevents the slide bite I occasionally got with the PX4, H&K P30 and Glocks. It seems like there's a lot more surface area on the CZ grip, which allows me to better support hand contact. I don't think the CZ's bore axis is actually lower. . . it just looks that way because of the reversed rails. I haven't actually measured tho. The PX4 requires additional texture in the form of Talon Grips or stippling. I'm OK with the stock P-09's texture.
Location of controls. Both are great. I like the PX4's slide mounted decocker better than I though I would. The huge OE decoker levers hit my strong side thumb every time the slide cycled unless I consciously re-adjusted my grip. The Stealth levers are too flat, making decocking awkward. The LTT's Fugly levers and their replacement solve that problem. The P-09's factory decocker works fine for my grip. The video above mentions that you need longish thumbs to reach the CZ's slide catch lever. I must have short-ish thumbs, because I have to release the slide with my support hand.
If you buy used, smokin' deals on Langdonized PX4's pop up regularly in the Classifieds. Hardly ever with the CZ's.
If you buy new, both are going to cost about the same to get it up to speed (from my perspective).
PX4: Aftermarket sights, Talon Grips, LTT decocker levers, TJIAB.
P-07: Aftermarket sights, Ship off to Cajun or CZ Custom for trigger work.
Adding a RDS to the P-07 is half the price of the PX4.