bonsai_enthusiast,
Your seedlings are OK for now, yes you will need to pot up but I don't see any urgency yet. Having roots grow through the mesh of the peat pellets is to be expected. The ones that emerge will die back but this encourages new roots to form along the portion of the root that is still covered. The roots will be more branched or ramified.
I usually start seeds in a small flat and transplant after a few weeks to individual pots. I use a more open mix that contains no peat, this allows me to easily remove the initial soil mix and make any necessary cuts to the roots. Usually this is
very minor at this time. I may nip the taproot or trim the ends of any overly long roots. Every time you re-pot is an opportunity to begin to shape the future nebari.
The bumps you noted are not branches. Future branches will form at the junction of the leaves and the stem, known as the axil. The structure may be a remnant of the germination process. I'll be doing some more soon and I'll try to be more observant.
All this overlooks your biggest problem though. Maples are a poor choice for indoor culture and I'm afraid you are going to have a rough time growing them inside.
Seedlings need a fair amount of light or they will grow tall and spindly. Unless you have a southern exposure I suggest you get a cheap shop-light with 4ft bulbs if you intend to have a serious go at this. Also, as you pot them up they will take an increasing amount of space and more effort to keep watered. You can probably get by the first season but come next fall you will have trouble providing the dormancy that Maples require.
How about a nice Ficus?
Norm