This is speculation, but I have occasionally come across the suggestion that Vishvakarma is another name for Brahma, implying that they are the same being. I don't know where this idea is from, because it is demonstrably not the case in the scriptures I'm very familiar with, but if there is any scripture out there specifically calling Brahma the divine architect, that could explain the timber thing, maybe.

Joseph Campbell said, "mythology is what we call other people's religion." If we were to go by that definition, the divide would always be subjective. More importantly, the wise will recognise wisdom, whether you label it mythology, religion or whatever, and the rest will see it as only stories either way. But I agree, it is bad form to call a particular living religion mythology, it reflects poorly on the person or institution saying it.

Also, having your religion labelled as mythology opens the door for people to learn about it in non-religious environments. That might be a silver lining.

(I did notice how old this post is)