Heating them together is usually fine in my experience, but storing them separately is a must. The pasta robs moisture form everything else, getting mushy and leaving the sauce dry.
If you really want one container to bring leftovers to work, put the sauce on the bottom add a layer of cheese, then put the pasta on top. Don’t mix everything until it is warm. You can get surprisingly ok results this way.
There’s no risk for a factory condition unit. This rumor started after people with units that had been dissasembled and reassembled had issues with vertical orientation. It turned out that it’s very easy to mess up the seals that keep the liquid metal thermal interface in place. So units that had been previously taken apart had liquid metal slowly leak, causing overheating and/or shorting.
If you haven’t taken the cooler off the mainboard, using the vertical stand is just fine. I haven’t seen any evidence of factory assembled units suffering leaking. It does imply that user servicing of ps5’s is a bit risky, and you might need to be wary of used units where you don’t necessarily know the service history.
To avoid unnecessary confusion, taking the covers off to add an m.2 ssd does not add any risk.