Perhaps rebbe could help - in trying to understand the mitzvah of trumas hadeshen and the way rashi presents the gacheles that fell from the mizbeach of 7b, it seems as though trumas hadeshen is a mitzvah in the kurban, but that seems hard to swallow, we have other sources that seem to indicate that trumas hadeshen is more of a mtzvah of the mizbeach.
Also there the achromnim indicate that Rashi Is saying that there is no mitzvah of trumas hadeshen for the eitzim, but there are 2 places on that daf where rashi says that the siyum of the mitzvah of the eitzim is trumas hadeshen.
Mordechai Soskil, Baltimore MD
About the Sugya in Meilah (I assume you mean 9b), I understand Terumas ha'Deshen to be an Avodah that marks the end of one day's Avodas ha'Mizbe'ach and the beginning of the following day's. Since it marks the end of the night's Avodah, any Evarim that remain no longer have to be burned. It is taken equally from the burnt remains of the Eimurim and the Etzim, as far as I know, and not limited to the Eimurim.
I am not familiar with the Acharonim you refer to; if you have in mind something specific please let me know exactly where to look, and maybe I'll be able to be more helpful.
Be well,
Mordecai Kornfeld