You can resolve the difficulties you raise here with the Tosefos Yeshanim on 38A, (3 lines from the bottom - Aval..) where he says there were two different kinds of maala ashan.
tuvya marcus, Jerusalem, Israel
(Please forgive the delay in response. Technical problems prevented the mailing of a number of responses.)
Baruch she'Kivanta! I found that Rav Elyashiv zt'l mentioned your idea in his He'oros l'Maseches Yoma, 38a, page 219, DH Omnam.
1) Rav Elyashiv said that the Tosfos Yom Tov and other Mefarshim (and that this is also the intent of the Tosfos Yeshanim here) write that there is an herb of Ma'aleh Ashan which certainly is essential for the Ketores. However, there is another choice species of Ma'aleh Ashan, which appears to be a sub-species of the primary species, which makes the smoke ascend in a straight line. This special species was not Me'akev but was merely a beautiful Hidur Mitzvah.
2) The craftsmen who were brought from Alexandria certainly included Ma'aleh Ashan. This ensured that the Ketores was valid. However, the Alexandrians did not know which special species caused the smoke to ascend straight up, but failure to go straight up did not render the Ketores invalid. Only the House of Avtinas knew which species possessed this special property.
3) Rav Elyashiv notes that upon careful reading, one will notice that Rashi (DH l'Ha'alos) hints to the above idea. Rashi writes that the Alexandrians did not know which herb caused the smoke to ascend in a straight line like a stick. It is clear from Rashi that it was only concerning this aspect that they were unaware, but they did know which herb was Ma'aleh Ashan.
Kol Tuv,
Dovid Bloom