CZ, early Sunday morning before placing phone calls...
Our Apples don't have that software loaded anymore so I don't have an "in front of me" test-case, but your description reminds me of the details. I'll try to call others who still have a similar setup to yours for 'practice', though.
You wondered if the printer could be defective, and you did what I'd have done - "Set extreme changes and see what happens" and it only revealed very minor adjustments.
But here's how all of our R-300-series died - we had about 120 among our customers, and all of them 'died' because of an overflow excess-reservoir that needed a $125 service call.
This is some sponge or tub that's hidden in the bowels of the printer, and it was simply emptied and some kind of 'reset fuse' was replaced and the printer would run and run and run. But this was such an angering and arbitrary contrivance by Epson to get us to spend money on their service-centers, and instead we'd get $100 Epson RX printers as replacements! Less money and no 2-3 weeks without printer!
None of them had "alignment" issues, if that's any help. That of course doesn't mean yours doesn't suffer from exactly that.
I have a vague recollection that once I thought I had alignment issues, but I decided to do a "Reset to Factory Defaults" on the printer, and then I uninstalled and re-installed all drivers and software. I remember some odd shenanigan like that once, but I don't remember if that was on a PC or a Mac.
More on this in about 7 hours...