If you have windows with wood interiors that can be painted, then you should paint them the colour of the trim. Normally you use the same trim colour throughout a home, especially when it's open concept as most new-builds are these days. That said, black windows are very fashionable, but only if the structure is very minimal. If there is any bulk to the appearance of the window, it would be too heavy a look for the interior. Without photos, I can't judge your individual case. I would not paint an accent colour (as you suggest with matching grey doors). Remember that you will be dressing your windows with a window treatment, so the window itself should read as a neutral element in the room.

I think it is fine if bedroom windows are painted to go with the room.