I suspect the rumor quoted in Rabbi Dov Eliach’s beautiful “Hagaon” biography the Vilna Gaon said the Arba’ah Turim was a “ספר משובש מאוד” is accurate. (Rabbi Chaim Kanievsky, though he originally gave a written approbation to the Sefer, was unhappy about this sentence after it was published (and two other small things), so told me a grandson of a certain close friend of Rabbi Kanievsky a few years ago.*)
The Beis Yosef, unlike the Kesef Mishneh, is constantly getting stuck on understanding what the Tur really meant. See for example the Perishah Y.D. 194:11 which the B.Y. seems not to have even thought of (although he surely saw the Agur quoted in Darkei Moshe).
The Bach, too; sometimes he edits freely, and other times he “says Peshat” (…!). How do they all decide which approach to use each time? I think the Tur itself is not mentioned as often or as prominently in halacha as he would have been, had the book been clearly phrased and well-edited.
(See also B.Y. Yoreh Deah 194 end of sub voce “Ain Ha’isha Teme’ah”.)
*Which, by the way, tells us how to judge Rabbi Kanievsky’s official, reported “retraction” of his Haskamah (approbation) upon the outrage expressed by Chassidim regarding the two chapters in “Hagaon” concerning the Vilna Gaon’s opposition.