I can confirm the change for Windows appearance in Mathematica 12.1 with, for example, your PresentationsPalette and Presentations stylesheet. Their windows are too large, but reducing their magnification makes the font size too small.
That is true, at least, for Windows running as a virtual machine (in Parallels Desktop) on my 27" iMac. But I don't believe that using the virtual machine makes any difference here: Windows is using the native resolution of my Mac.
Usually I'm running Mathematica 12.1 directly on the iMac, and there the palette sizes and stylesheets seem OK.