it’s fine man. you can transplant now or wait a little, it isnt root bound or anything. Dont worry about disturbing the roots, if they break off or whatever it wont hurt it at all. They can take some rough stuff.
For sure, nevermind those runner roots. Always remember,...... top growth is a direct reflection of root mass/ health/ development. When in doubt... wait it out!
If you keep them in another sealed cup the moisture inside will draw the roots out into it. If it's open the roots will air prune and fill the medium instead
Don't get too caught up with light touching the roots. Imo it doesn't matter much. The only issues you will come across is algae.