The gemara cites a braisa with many different opinions regarding the type of learning a ba'al keri is allowed to do. The concept seems to be that if the learning is too involved or based on pesukim, it is not allowed. Whereas superficial type learning is allowed, but they argue where exactly to draw the line. The opinion of R. Yehuda is that a ba'al keri can study hilchos derech eretz which is halachos about appropriate conduct for a Talmid Chacham. The simple reading of the gemara is that the reason R. Yehuda allows the ba'al keri to read shema with brachos, is because he considers it like hilchos derech eretz.
However, the Tzlach is meda'yek from Rashi עשאן רבי יהודה - לברכת המזון, that this concept of being like hilchos derech eretz doesn't apply to krias shema and birchas krias shema, and doesn't even apply to the birchas hamazon after the meal. What does it mean that R. Yehuda considers the saying of these things to be like hilchos derech eretz? The Tzlach explains that this can only apply to the bracha rishona that one makes on food which is learned from a sevara that one cannot benefit without thanking Hashem. When Rashi says Birchas HaMazon, he means bracha rishona. A bracha before eating is exactly like hilchos derech eretz. Therefore it comes out that for d'oraysa things such as shema and birchas hamazon after eating, R. Yehuda will say that one can even say them since he holds that hirhur is not like speaking. When it comes to bracha rishona, one is allowed to actually say it since it is like hilchos derech eretz. And for birchas krias shema one is only allowed to be meharher.