I have a question on 39b the gemara brings a machlokes between R Yochanan and R Huna what do we make a brocha on first is it the pieces of bread that are bigger or is it a whole piece of bread even if it's smaller? And R"Y holds that the whole is more important and we make a brocha on it first, but even he agrees that if the not whole piece which is made out of better flour we are mevorech on it first.
The Gemara then brings a k'Tana'i and it seems to me that according to Rashi we're asking on the part of the Gemara that everyone agrees that we're mevorech on the pure flour bread first.
But I'm not sure what exactly we prove with the Machlokes that we bring which talks about onions do we give a small whole onion to the Kohen for Terumah or do we give a bigger half of an onion, if according to Rashi we're trying to ask on the flour type that everyone agrees about, then why would we attempt to ask from smaller whole and bigger half of an onion, but by whole and bigger R"Y argues and still he admits by a slice of wheat bread?
A simplified answer to your question is that when the Gemara says a "small onion" and a "big onion," it does not merely mean a difference in size, but also a difference in the quality of taste. The big onion is a type of onion that is tastier than the small onion. This lends itself to the piece of the big onion being possibly more important than the whole small onion, similar to the discussion regarding wheat and barley. (While Tosfos seems to say that Rashi is not taking this into account, the Pnei Yehoshua says that Rashi does.) The true answer to your question, meaning the intent of Rashi's understanding in this Gemara, is discussed at great length by the Pnei Yehoshua.
All the best,