The twins will probably fight for space in one pot and it may mean poor growth for both of them. It isn't as traumatic as it may sound to separate them. When I did it there were two tiny but distinctly individual root systems. It's obviously up to you but if you do go for it, it is better to do it sooner rather than later.

I got a bit of stretch from my seedlings too, I buried up to about 1cm below the cotyledons, which I believe is only really OK to do early on when the stem is thin and soft, after which rot is a concern. I second the fan idea. It will toughen them up.