I really don't think the scientific method is a subjective thought, is it? Or do you mean simply that it is a human construct and therefore has a subjective foundation?
Of course, the hypotheses that the method is used to test are frequently highly subjective. But I don't think that matters, exactly, because what matters is whether you can find measurable proof, or not. And then you can talk about whether your measurable proof is repeatable, or whether you really measured it effectively, or whether you have actually found anything worth finding. It should really be only a starting point.
Applying the scientific method to God's existence, however, is explicitly ruled out by Deuteronomy/Luke ch 4 I guess. Which does make me feel a bit 'He would say that, wouldn't he'. It certainly means that there is a spiritual exit strategy whenever God does appear to fail a scientific test. I see the point that applying the method to Him rules out transcendence. I'm just not quite sure what we lose if we don't have transcendence.
If a majority of people who see visions turn out to have a specific form of 'epilepsy' or 'mental illness', does that matter? To me it does, rather, living as I do with someone who has schizophrenia and whose visions can be highly inconvenient for me. But that's only a label - no doubt he would rather be seen as a visionary, and that might be a more helpful life role for him.
If the linguistics of speaking in tongues is studied (which is has been, I read a very good Christian article about it) and it is shown that nobody in those studies ever used vowel sounds that were not in a language they already knew, does that matter? The author discussed this and said that he believed those speaking in tongues were in an open spiritual state which had benefits for them and their church community. Essentially, 'whether it's true or not, it's still helpful'.
I tried to attend church for three years in the 'whether it's true or not, it's helpful' frame of mind, but I found in the end that I simply could not stand up and say the Nicene Creed every week in that scenario. Whatever Dawkins says (he's quite nice about theologically sophisticated Anglicanism in GD I think), and whatever Rowan Williams says about 'that's not what Christians really believe' and whatever furious articles appear by clergy saying how OUTRAGEOUS it is that people think Christians believe in an afterlife.... if you go to a bog-standard parish church and listen to the sermons every week, you are supposed to join in with the Nicene Creed and you are highly likely to hear statements such as 'Unless you believe every word of the Christmas story, there is no point in you being here.' (direct quote). Impasse.