Is it normal for a bathroom rough-in to take three visits and have this many mistakes?

You aren't overthinking this. In fact, that ProPress fitting sticking out past the stud is a major red flag because it shows the guy isn't even checking his work with a straightedge. Once that drywall goes up, you'll have a massive bulge or the board will crack trying to screw it in. That needs to be cut out and recessed properly before the rock goes up. And the excuse about the brass Baril drain rusting is complete nonsense. Brass is used specifically because it doesn't rust, whereas the cheap ABS kit he used is just a way to save time and effort on the install. If you paid for high-end trim, you shold get the brass assembly installed.

That notch in the 2x8 joist is also a serious concern. Code generaly says you shouldn't notch the top or bottom of a joist in the middle third of the span, and even then, a 1 1/4" deep notch on an 8-inch joist is pushing it. If they keep hacking away at that structure to fit a drain they didn't plan for properly, you're going to end up with a bouncy floor or a cracked tile job in six months. You need to stop them from removing any more wood untill you have the owner look at it.

As for the PEX stub-outs, it sounds like he's just being lazy with his measurements. PEX is great for speed, but if it's flopping around or sticking out six inches from the wall, it looks like a DIY disaster. They should be using **drop-ear elbows** or copper stub-out ells that are braced to blocking so the toilet shutoff is rock solid. A plumber who misses the tub spout entirely on the first pass is clearly checked out. Call the owner and tell him you want him on-site for the next visit to audit the rough-in. You're paying for a professional job, not a training session for his apprentice.

That PEX sticking out for the toilet is a classic sign of a lazy job. If it’s just dangling there, your finish trim will look like garbage and move every time you touch the valve. Tell that plumber to use HoldRite Stout Brackets to secure those lines. I use them on every single bathroom becuase they lock the pipe in place so it’s rock solid behind the wall. It sounds like this guy is skipping the basics to save five minutes. If he’s not using proper support brackets, I’d be terrified to see how he’s supporting the actual shower valve.

Have you ruled out the possibility that the brass waste kit didn't actually line up with the overflow angle on your tub? I've seen guys swap to ABS when the brass shoe is too short or won't seal right on a specific slope, even if the 'rust' excuse was just a bad way of explaining it. Also, regarding the joist, did you ask if he's planning to sister it or use a steel plate? Sometimes they cut first and reinforce later once the pipe is set. Three visits is a lot, but is this a standard layout or are you doing something custom that might be slowing him down?

Honestly, the fact he missed the tub spout entirely is the biggest tell. That's not just a 'whoops' moment, it's a sign he doesn't have a plan. I'd be checking the vent pipes too. If he’s hacking up joists and forgetting basic lines, I'm betting he didn't slope the drain right or didn't bother venting the sink properly. Don't let 'em close those walls until you see water running through it and check for leaks yourself. That guy's defintely just winging it.