Daf Yomi - Yoma 53 - Ketores Missing Ingredient

The Gemora states that if the kohen Gadol enters the Kodesh Kodoshim with the ketores and he is missing one of the ingredients, he will be חייב מיתה. The Gemora proceeds to ask, that he will be חייב anyway because of the prohibition of entering the Kodesh Kodoshim unnecessarily (for he did not fulfill the mitzva of ketores)?

In the Sefer Yam Hatalmud, he asks based on a Gemora in Shevuos, which learns according to the opinion of Rebbe that Yom Kippur will automatically be mechaper for any aveiros that are not specific for Yom Kippur. If so, what is our Gemora asking? If the issur is burning the ketores when it is missing an ingredient, this is an issur exclusive to Yom Kippur and he can be punished for it, but if the issur is entering the Kodesh Kodoshim for no reason, that is relevant the entire year and Yom Kippur will give him an atonement immediately? (See שמועת חיים for a possible answer.)