After he showed him what a beinoni of Tanya is (someone who has a yetzer hara but never does any aveira, big or small,
I admit unfamiliarity with mesillas yesharim but based on what I do know, what you describe is the norm. There are the born tzaddikim who are the rare exception (such as Moshe rabbeinu who was born mohul, which is apparently can be a sign of such),
Moshe rabbeinu worked on himself to make himself a tzaddik (maaseh where they brought someone to draw him)
Additionally nowhere does it term benonim in Gemara like you, Benoni could be either someone that is “50/50” or someone that has at least one mitzvah
We say Yosef is Yosef hatzadik because he was עומד בנסוין yet there are four people who didn’t sin and only died “because of the נחש”
And I highly doubt the בעל התניא thought he was a בינוני