The Aruch HaShulchan points out in the first siman of hilchos rosh chodesh that the 2 day rosh chodesh that we observe on every month that is 30 days, dates all the way back to the time of the nevi'im. Our minhag is to treat both days as rosh chodesh by abstaining from tachnun, saying hallel and even davening musaf of rosh chodesh (which is related to the korbanos).
Based on this, Rashi in our sugya is very difficult. The wife of R' Eliezer would always stop her husband from saying tachnun (nefilas apayim) out of concern that the power of this tefillah would penetrate the heavens and lead to the death of her brother Rabban Gamliel. The gemara says she got confused between a 29 day month and a 30 day month. She thought it was rosh chodesh when in fact it was not, and thought that her husband wasn't going to say tachnun due to rosh chodesh. In actuality it wasn't rosh chodesh, so R' Eliezer said tachnun and Rabban Gamliel died. Rashi explains that she thought it was a 29 day month so that Rosh Chodesh would be on day 30. In actuality it was a 30 day month so that rosh chodesh was on day 31. She didn't prevent her husband from saying tachnun on day 30 thinking it was rosh chodesh, but since it wasn't he said tachnun and caused Rabban Gamliel to die. Rashi clearly holds that if rosh chodesh is on day 31, tachnun would be said on day 30. This contradicts our minhag which the aruch hashulchan claims dates back to the time of the nevi'im to keep both day 30 and day 31 as rosh chodesh?