For me, it's simple-- for pursuits that are rational, I trust my intellect and the scientific method. For pursuits that are instinctual or irrational, I trust my gut.
I'd never "go with my gut instinct" to solve a complex mathematics problem. But I'd never use reason or the scientific method to fall in love--with my wife and I, we "just knew". We celebrate 12 years next month.
Music-making is for me very much more like falling in love than like solving a mathematics problem. So I tend to trust my gut a lot. However, there are many pursuits adjacent to music, and which work in support of music, that are a lot more like solving mathematics problems. But which-is-which, or where the line is drawn, can be reasonably contested by reasonable people.
Where each of us makes the distinction between the two mindsets is probably up to our individual experiences, priorities, personalities, etc. Some people might choose instruments and tools based on study of specifications. I tend to prioritize emotional connection over even technical suitability, most times--I don't care if the 2017 Telecaster stays in tune better, is quieter, and has measurably lower action and better intonation than the 1954 blackguard. If I pick up the 1954 blackguard and FEEL something more, then that's the better guitar to me. Even if it's based on nothing that can be empirically verified.
And I do think it's important to make a distinction between that set of priorities and "magical thinking." Because it's sentimentality, perhaps, but not self-delusion--at least not in every case. And I think artists and musicians can be forgiven for being a touch sentimental. It's one of the things that makes us suited to connect with audiences on a feeling level.