krias shema - d'oraysa or derabbanan?

There is an opinion of Tosfos (Menachos 43b) which holds that krias shema is not a mitzvah d’oraysa, contrary to what most of us probably assume without a second thought. Because of the many proofs that reading krias shema is in fact a kiyum d’oraysa (see Tosfos Sotah 32b which lists numerous gemaras that point in this direction), the Sha'agas Aryeh concludes that everyone must agree that there is a mitzvah to read parshiyos at morning and night, b’shachbecha uv'kumecha. The only question, says the Sha’gas Aryeh, is whether the specific parsha (or parshiyos) of shema must be read, or whether m’doraysa any parsha may be read, and the designation of reading specifically the parsha (or parshiyos) of shema is derabbanan.

My wife’s grandfather, R’ Dov Yehudah Shochet, in passing in an article on a different topic mentions a proof to this Sha'agas Aryeh. Tosfos (Menachos 66a) writes that sefirah is only derabbanan, and since sfeika derabbanan l’kula, once may count during beis hashemashos, the time period of safeik day safeik night, without waiting for actual nightfall. Were krias shema really only a kiyum derabbanan, the same logic should apply; one should be allowed to read shema during beis hashemashos as well, without waiting until tzeis. Yet, the very first Mishna in Brachos tells us that the time for krias shema is tzeis, not earlier! It must be that the Sha'agas Aryeh is right -- everyone agrees that there is a mitzvah d’oraysa of some sort; the only question is whether a specific parsha is mandated or not.