Oh, I'm so happy that it's working out for you! I tend to cheat on the towel - I'll let it go for a few days because with the heating pad on the mess dries up really quickly, so they aren't standing in wet poop. Then I'll take the towel out, give it a shake to get the loose stuff off, and fold it with the soiled side in and put it back on. Next time I just toss the towel. (This is when it comes in real handy to hit a Goodwill or other thrift store and buy up a bunch of threadbare towels that you don't mind losing!) When they were little, I used Press 'n Seal on the top, but when they went outside that was just too much fussing, and the poops are so much bigger when they get older!. So, like I said, I turn the towel inside out (be sure you don't just flip it over and end up with all the poop sitting on the heating pad!) and put it back. I also heaped straw on top of the heating pad and towel, but they love to scratch and it all disappears!
Chicks and chickens usually start heading for bed just before or as it gets dark. Once they are bedded, they barely move. I'm sure they can see in the dark, but because they "hit the hay" early and sleep pretty soundly, very little disturbs them. So whether they can see or not really doesn't matter....they aren't moving!
That's why most of us do whatever catching, moving or adding chicks to a broody we need to accomplish in the dark. They barely flinch!
Mine seem to accept us hanging around them better than my other chicks did last year, and I think it's because they aren't constantly being fussed at and, like you said, having hands reaching into the brooder from over their heads. Lots of folks accomplish the same thing by having a regular brooder that's above floor level and can be opened from the sides rather than the top. But I think the biggest difference is that they know they have that security of the warm, dark cave to scoot under, rather than just running around a lit up brooder and trying unsuccessfully to find a way away from what's scaring them. Builds confidence!
Congrats on having such a smooth transition. Wait until you try it from day one! It's amazing!