There is a rule 'תדיר ושאינו תדיר, תדיר קודם'. Loosely translated: When faced with two mitzvos, one must first perform the one which occurs more frequently.
Q: When it comes to bracha achrona, we find the custom/halacha to contradict this rule.
I believe borei nefashos is considered tadir regarding al hamichya based on the fact that most people make bore nefashos more frequently than they do al hamichya.
I also assert that one blessing can be categorically more todir over another [even regarding blessings which could come any time and have no קביעות in their תדירות] just based on how frequent they actually are.
I support my position with the Gemara (Brachos 51b), which classifies Borei Peri Hagafen as more frequent than Kiddush. The Ritva (ad loc) discusses the תדירות of Birchas Hamazon v. Borei Pri Hagafen, both of which are not limited to any specific time and are constantly possible. The Magen Avraham 165.3 writes that asher yatzar precedes borei nefashos because of todir.
And yet, the prevalent custom (in accordance with the Pri Megadim [OC"H AA, 202.25], quoted by Biur Halacha) is to preceed al hamichya to borei nefashos. Is there any rationale to why the rule of tadir kodem doesn't apply?