The gemara cites various opinions as to when it would be permitted to eat chodosh nowadays, depending on whether it is d'oraysa, and depending on the institution of R. Yochanan Ben Zakai who held that the entire day of the 16th is assur. The gemara explains that the opinions who aren't concerned for the sfeika d'yoma must hold that the issur chodosh in chutz l'aretz is only d'rabonon, therefore mi'safeik it is mutar. However, the final opinion in the gemara is that chodosh is assur m'doroysa on chutz la'aretz and is assur without a beis hamikdash the entire day 16, therefore is assur nowadays until nightfall after the 17th of Nissan. This is paskened in Rambam and Shulchan Aruch at the end of hilchos pesach. The Rambam refrers to the issur through the 17th as "divrei sofrim" rather than a s'feika d'yoma because nowadays we are experts in when the actual rosh chodesh is and only maintain the original system based on מנהג אבותינו בידינו. The Rambam seems to refer to this "minhag" as divrei sofrim.
The Mordechai (Beitza, perek 1) asks that we have a rule that דבר שיש לו מתירין is assur even when it is just a safeik. Why does the gemara have to say that chodosh is assur on the 17th since it is d'oraysa and we are concerned for the sfeika d'yoma, even if it's only d'rabonon we should be concerned for the sfeika d'yoma? He answers that since the issur comes again the next year, it isn't considered a דבר שיש לו מתירין. The Achronim ask on this Mordechai that the grain which became mutar this year will never become assur again, therefore we should consider the grain of this year a davar she'yesh lo matirin and say that it is assur m'safeik, even if the safeik is d'rabonon? The Cheshek Shlomo (R. Shlomo Vilna) answers that the safeik of chodosh is not on the grain, rather it is a safeik on the days whether the 17th is still assur to eat chodosh. Had the safeik been a safeik on the grain, it would not be considered a safeik that is חוזר לאיסורו but not that the safeik is on the day, it is considered a safeik that will return next year until we start sanctifying the new moon through witnesses. The concept of דבר שיש לו מתירין only applies when the issur happens to occur but not when it is an established system that will return year after year. Therefore, even though the actual grain will never become assur, it is regarded as a דבר שיש לו מתירין.