Reb E, hachanah from shabbos to yom tov and vice versa is regarding the pasuk of vehechinu, that one must have all the necessary foods one will use on yom tov available to him at the onset of YT, and not that it should be nolad(not in existence at bein hashmashos), or in a state of unavailability (grogros utzmukim).
Those issues have no bearing on, for instance, making beds a few minutes before shabbos ends, speaking out plans for melacha to be done after shabbos, etc… that’s a derabonon issue of dabeir davar. The siddur shailoh has nothing to do with hoil and “hachanah derabbah” as the poskim refer to it.
We pasken there is no muktzeh at all on shabbos (baya 2b). Yet there is the other type of muktzeh (tiltul).