The cups/collars were just to contain water from the sprinkler system escaping. I would lose 500 ml or more per day without them. I cut the tops off the cups thinking this could perhaps avoid rot if the leaves touched the sides. It all worked out fine so I left it as I did without any further adjustments. I never considered them to be domes.

I also have some clones cloned in an ice cream box filled with water and under a dome. They have been very slow to root and needing the dome for at least a week after potting them into soil. They will droop in an hour without the dome, and get back to normal in an hour if I put the dome back on. Quite interesting to observe. 

I use a water pump btw.