May one place a siddur on top of a cover of a sefer torah or is it forbidden just like one may not place a klaf of nevi'im on top of a sefer torah?
Answer:
It would not be permitted to place a siddur or a chumash on top of the cover of a sefer torah.
Sources: The cover of a sefer torah has kedushah, and its level of kedushah is one level below the kedushah of neviim and kesuvim, or the kedushah of an invididual chumash if the chumash is written by hand on kelaf (Shulchan Aruch, Orach Chaim 153:2). A siddur (and even a regular chumash, see Mishnah Berurah 153:6) does not possess this level of kedushah, and it would be forbidden to place it on the cover.
[See Magen Avraham, 153:2, who writes that even when two levels of kedushah are equal, it is permitted to place one item of kedushah on the other only because we cannot avoid it.]