After reading through a couple of motherboard manuals it seems that, at least in that small sample size, any additional mechanical x16 slots are connected to the chipset and therefore independent of the CPU lanes. The boards I had a look at had the second x16 slot running at x4, which isn't a problem in this case.
Anyway, YMMV, study the manual of your motherboard.
Yep, in this case I'd just read the manual religiously to make sure the board could support all the IO + graphics lanes you need. Watch out for the common gotchas, like M.2 deactivating x4 or multiple x1 lanes, etc. x570b would give you more PCIe lanes to play with, but it's definitely possible to find a B550 board that could do this. Also check rear iO and make sure you aren't losing too many USB ports there to allow for more PCIe connectors on the board.
650 W on the power supply ay be a little tight. Depends on how much wattage your peripherals on USB draw and how effective the 480 underclock is. Definitely doable tho, just keep an eye out for system instability of course. If you see any of that behavior, you will have a likely culprit.