Hello99,
I managed to find the Pri Chadash inside, and he says that the karaim are considered the same as mechalelei Shabbos because they are mechalel Yomim Tovim. He definitely seems to be toleh it on chillul Shabbos. I see no reason to think the Pri Megadim didn’t see the same version of the Pri Chadash as we have (I don’t know what to make of his statement that they don’t eat our bread; it’s probably a way to express that they don’t have the status of Yidden).
Hello99, can I ask you a favor? Do you have a list of mareh m’komos to learn the inyan of muktzah?