Hi! Welcome!
It is always an interesting decision, isn't it?
There is another 'clipping top knot' thread (as in trimming)...have you had a chance to check it out? Actually, there are at least 2 of them which discuss the same sorts of things.
You, of course, could trim, clip, or band the top knot. You can use a band to push the top knot back a little over the head, or pull out some hair from the band on the front to create a poof and push the hair back. You could clip the hair short and not worry about a top knot at all.
I would not leave anything in my babies' hair that could harm them...if they ate it...when I am not with them. I would not expect a tiny non-latex band to be harmful like a metal clip would be, so mine will only have metal clips when they are basically in my arms where I can watch them closely.
Have you thought about what you want your baby to look like? The decision is really yours, after all. Your decision will influence greatly what you use in your baby's hair.
Take care!