Root Through Cup

So I'm doing a super simple, one light grow with 5 plants. Objective is to end up with a Bonsai Mom or two. Not harvesting, just growing a bonsai.
Went with clear cups this time so I could actually see how wet/dry the entire cup of soil is. Using two cups for each plant. One with holes in the bottom, sitting on a hole drilled spacer, inside another cup that acts as a drip catcher.

Keeping notes everyday and physically checking each cup out as often as possible. Just notice that #5 seems to have the tap root through the bottom of the first cup? On day 4 of popping through the soil after 16 hour water germ. Is this root sticking out the bottom going to be an issue ? Probably should have used some fine mesh on the bottom of the cups to prevent this but these things germed so fast, I wanted to get them into soil. No nutrients at this time, strictly RO water, as the last experiment went poorly by feeding too soon. Should I try and put it back up inside the cup ?

It wont be long and roots will be growing out the bottom to get that water. No problem at all. You might get some green algae or some greening of the actual roots if the roots ar weeds getting light, but agsin nothing to worry about. Its neat pushing the plant. I'd like to see how it turns out.