The state of most windows (like item properties) are saved globally, not as part of individual project settings. That's always been the case. In most cases, if you have the item properties window open (and perhaps docked somewhere), that's the way you want REAPER to look, not the way you want one individual project to look.
You can save/load window states as screensets if that helps you.
Item Properties - hide state is broken
Linear Mode
