For me it's not just that trek presents mysticism as having a scientific grounding, it's about how it values the two. Commonly our heroes walk away just as ignorant about the abilities of the likes of Q, Trelane, the prophets, whoever as we are. The advanced science as magic trope clearly does apply.
However (and this is a big however), failing to find the implied scientific explanation for every little mystery does not detract from the way those "magical" beings are de mystified, reduced to fallible agencies which can be dealt with using reason. We may not come away knowing exactly how they manipulate subspace or read minds but we do get the message they are not to be treated as gods.
Starfleet may not be able to reproduce or even explain their exploits but they don't really need to for the show to work. All that is required is that we keep seeing that which at first appears divine shown to be flawed. "Gods" are shown to be fickle, petty, cowardly or false, even if we accept them as being currently superior in some sense the key word is "currently". The Metrons and Q clearly state they foresee humanity surpassing them, Apollo only enjoys his divine status whilst humanity is earth bound and unable to meet him amongst the stars, where he is shown to be not only mortal but painfully vulnerable, not quite a pretender but a showman and braggard.
Conversely V'ger is vastly superior to humanity in terms of technology but it's crucial flaw lies in defining it's purpose in terms of it's maker, seeking out an imagined greater being when the answers (or at least the right questions) lie in human reason, in rationality, in the tendency to ask the universe questions directly rather than expect some higher power to supply those answers.
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