I suspect the culprit is UA's (CO's) lousy IT system doing the forcing of the CA flight into a Y booking class. Maybe they just didn't load the entire range of CA fares into the system. If your trip is more than 3 months out, it could be because CA hasn't loaded all the discounted fares into its system yet (usually fares are loaded quarterly). In which case the placeholder Y fares are all that UA would be able to access and book right now.
Be that as it may, booking separately is an acceptable (probably better) strategy, and on paper at least, these long layovers in Shanghai are more than enough. I say "on paper" because if you've been following UA's woes, you'll no doubt be aware of the huge problems they've had on the PVG-USA routes, including the one that stranded passengers for 3 days at PVG. The Chinese domestic side isn't a problem.
Make sure that you know what airport you are departing to/from for the domestic. Since you're obviously going into the city and presumably staying somewhere, I suggest that you make the domestic flights from/to SHA (Hongqiao) not PVG. The airport switch isn't an issue with Shanghai stays scheduled like this. And you'll have more choice of flights out of SHA.