All the advice and tips given so far on cloning have been correct, and your gut was correct. I know I like to hear it summed up and said sometimes, so let me see if I can do it for you:
1 - The point of the dome is to keep the plants from transpiring after being cut. They have no roots to bring up water. This is also why you cut the bigger leaves. You do not want to leave the dome on seedlings or rooted plants simply because of all the reasons you wouldn't want your whole room at 90% humidity and 80 degrees.
2 - The guideline for when to transplant is when you see a few roots and/or new growth A subjective measure, but as soon as I see enough roots that I feel like the plant could survive I get it into the next medium and on its way. Every day it stays in the dome won't hurt it necessarily, but its not getting all the juice the next level up gets. But make sure you see roots, cause if there aren't roots - the plant will shrivel and die in a day outside the dome. I had this happen recently - 1 out of 30 so far. It was green and nice under the dome,one day out and I did not catch it that day, and by the next morning was dry as a bone.
3 - Newly vegging straight out of clone plants are peachy. If they have the roots - give them your regular healthy starting veg formula and let them go. They are healthy plants ready for love. I've only had 3 cycles of clones, but every single one has liked the move from dome to veg - they take off. 1 in 30 casualty ratio.
All that to tell you what you already knew.
