Haha yeah I had one of them do that, I figured by the time it switched to flower it would be 3" tall
so it got kicked to the curb.
I have yet to have a problem with the roots breaking through the jiffy lining but who knows.
What light schedule are you on? Do you pour water over the hydroton daily to keep them nice and wet? Not sure if you are supposed to but I always have and have yet to experience any negatives from it.
I am at around 18 days from when I placed it in the napkin to sprout the seed.