My main concern is twisting of the roots, not so much the discoloration.
You’ve got no control over the roots twisting. Keep the cover on and let her do her thing.
Oh and from my experience, the only real time root twisting comes into play as a problem is when we start in a solo cup and let her go too long, that root twisting is then called “going root bound” and that is when those roots twist all round that solo cup and can’t go anywhere else, no more place to grow, thus root bound. Never wait too long to transplant. Always err on the side of caution, if you think she’s ready transplant her. You will get better by lifting the cups when they are full just after watering, and throughout till she’s dry. A moisture probe will help you perfect this technique. Cheers!!