Answer

It is not right to try to reconcile things if you are certain — or even think — that the reconciliation does not actually fit the author’s view. That is just empty pilpul (or creating a new approach of your own, which is legitimate in itself. But it is not Maimonides’ approach). Therefore, when the answer is forced or overly convoluted, it is unnecessary. The conclusion in such a case is that the medieval or later authority under discussion probably made a mistake (in my opinion). If you prefer to be modest or polite, remain with “this requires further examination.”
But when the reconciliation is reasonable and has support from other places, there is no reason not to do it. In this context, it is worth mentioning regarding your common claim about Maimonides’ commentators, that in my opinion it is mistaken. Even if Maimonides did not use the terminology and mode of thought of Brisk, that does not mean that a Brisker interpretation of his words is wrong. If he had known that terminology, perhaps he would have agreed that this is in fact what he meant. It is possible that he would even have admitted that this toolbox would have helped him formulate better what he himself wanted to say. Like that midrash about Moses sitting at the end of twenty rows in Rabbi Akiva’s study hall and understanding nothing, until they said, “It is a law given to Moses at Sinai,” and his mind was put at ease. Of course, that does not mean they are always right (they are not). But it does mean they are not necessarily wrong. Every interpretation has to be judged on its own merits.
There is an interesting dispute on the question of the truth of Brisker interpretations of Maimonides (those two views I mentioned — yours and mine), between Rabbi Yehoshua Hutner (founder of the Talmudic Encyclopedia) and the author of Seridei Esh.