I don’t know if the OP still cares about this thread, but I’m going to chime in with my thoughts on the matter anyway.
I think it’s fine to pick the gender of the MC but when supporting characters are being considered I think it would be better to already have a clear vision of who you want them to be. I think that they should already be pretty well developed when you introduce them to your story. I believe that gender is a big part of their identity in this sense; when you picture your supporting characters how do you see them?
I’m starting to outline my own story and when I think of my supporting characters I first visualize how they look and from there I would develop the characters background, personality traits, quirks, and goals. Of course I would leave room for them to grow as characters through out the story, but I would like to have a real sense of who they are before they are introduced.
The only one I can see no problem with swapping gender is the MC. The reason being that this is essentially your avatar, your way of interacting with the story. I think the reader should have a say in determining who they are while exploring the world you’ve created, but the supporting characters should remain how you envisioned them. While the MC is the vehicle that drives the plot forward, the world and the characters are the reason the journey exists in the first place. I believe that it’s up to the author to create the journey but it’s up to the reader to determine how they get to their destination.