On the level of pshat, it’s probably true that the mishna means that the mitzvos above can be pushed aside by talmud Torah. But there’s always more than one way to read a mishna, as they were encoded by Tannaim to include as much as possible in the shortest space. Although there is no “drush” in mishna, I would agree that the tanna could be hinting to the idea that Torah should be k’neged the other mitzvos, and that one should perform them specifically according to the rules of the Torah and not be negligent in them. We see this use of k’neged in many places to mean “adjacent to” rather than “opposite” and it could be that the Tanna wanted to be marbeh this possible interpretation.
Also, Torah should be k’neged the other mitzvos in that gradeh if one is learning he doesn’t need to worry about how many mitzvos he’s passing up at that moment; but one shouldn’t make an “escape” out of learning that he runs to his private corner whenever an opportunity to perform a mitzva comes up. He should put his Torah kneged the mitzva: run to the mitzva, and then to the sforim.
Nice pshat!