The simple reading of the mishna implies that both R. Meir and Chachamim agree that the shechita of a child is invalid so that there is no requirement to cover the blood, yet in the end of the mishna the Chachamim hold that if a חרש שוטה וקטן shechts the mother, one cannot shecht the child on the same day because we are concerned that the shechita is actually valid. The gemara discusses why the Chachamim would be more strict to forbid shechting the child on the same day than with the mitzvah of covering the blood, and ultimately cannot come up with any rationale. This forces the gemara to conclude that the Chachamim would indeed argue by the mitzvah of covering the blood as well, and would require the blood to be covered after the shechita of a חרש שוטה וקטן. Tosafos raises a very interesting question. There seems to be a very obvious distinction between the mitzvah of covering the blood and the prohibition of shechting mother and child on the same day. It is typical for the Rabbonon to uproot and be passively be mevatel an aseh, a positive mitzvah, in order to preserve a negative commandment and prevent it's violation as they did with shofar on shabbos. Therefore, it is perfectly logical to absolve the shechita of the child from the mitzvah of covering the blood (note: the mitzvah couldn't be on the child, rather on those watching as rashi writes), in order to preserve the prohibition of neveila because if they would require the covering of the blood it would mislead people to thinking that the meat was kosher. However, in the context of אותו ואת בנו, it wouldn't make any sense for the Rabbonon to absolve from the prohibition of אותו ואת בנו and permit the slaughtering of the child in order to preserve the prohibition of neveila. Why would they be more lenient about one negative commandment in order to preserve another? Tosafos suggests that in truth the assumption is that the animal is a neveila and there is no mitzvah of covering the blood and no prohibition to shecht the child. However, being that there is a small chance that their shechita is valid, it would have been worthwhile to cover the blood on the off chance that the shechita was valid. Yet, the Rabbonon didn't want this done because it would mislead to the eating of the animal. Similarly, the gemara asks they should have been concerned that being machmir for not shechting the child (which is not technically a concern since we assume their shechita was invalid), would lead to the eating of the animal (which is really assumed to be assur). That is why the gemara understands that there shouldn't be any distinction between the reisha and seifa of the mishna. It seems to me that Rashi would not be able to use Tosafos answer. Tosafos answer is predicated on the premise that the animal shechted by a חרש שוטה וקטן is really a neveila, not just a safeik and therefore a more real concern than אותו ואת בנו. But, Rashi (ד"ה מאי שנא, וד"ה לחומרא) seems to view it as a regular safeik according to the Rabbonon whether the shechita is valid. Therefore, Tosafos question comes back. It seems to me that the rationale as to why the gemara felt it would make sense to be more concerned with the safeik of neveila, than with the safeik of אותו ואת בנו, is because if we were to do something that would indicate the neveila was permitted to eat (such as cover the blood or abstain from shechting the child that day), one would definitely eat the neveila. There would be no question that one would not want to waste meat that seemed permitted and would definitely use it, therefore by permitting neveila it would unquestionably lead to the issur. Whereas saying that one may shecht the child on the same day will not definitely lead to an issur, since the owner would only shecht it if he actually needs it. Therefore, it would make sense for chazal to ignore the issur of אותו ואת בנו if by being concerned for it would lead to the violation of eating neveila.