I keep mine in the refrigerator once I open it since I worry about aflatoxin - realistically a jar probably doesn't last long enough around my house that that's a real worry, but better safe than sorry IMO.
It varies a lot from brand to brand, and sometimes even from batch to batch within a brand, just how much oil is in each batch. But yeah - taking it out of the fridge ahead of time, or just spooning whatever you plan to use onto your plate and letting that warm up before spreading - that helps. Or, since I have peanut butter in hot cereal much more often than I do on bread, I'll just nuke the cereal for 20-30 seconds after adding the PB, to warm it all back up.
The other thing I do to help mix a jar that's been on the store shelf long enough to separate, is as soon as I get it home, I put it upside down on the counter. Leave it there until the oil is at the other end (opposite the lid). If the jar is really old, I might do that a couple times each side before attempting to stir it. Stirring with a knife rather than a spoon is less messy IME - I can kind of stab the solid parts to break them up, and mix with more of a gentle churning motion than a circular one, at least until it starts to get smoother. But it sounds like you're already doing that.