Then let us think about the question in a way that isolates and addresses your stated problems. Too much root growth for the required veg time from seed and seeds need a minimum time to become mature enough to flower.
My first thought is that as you are growing HPA you do not need a taproot, which is one of the main reasons to grow from a seed. Instead, you actually want the sort of lateral root growth you get from clones. Lots of fine roots spreading out almost horizontally from your stem.
Additionally, using clones, you can go straight to flower once rooted although 2 weeks veg gives greater benefits (depending on your grow chamber size). I run clones and I give them between 9 and 14 days veg and with between 8 and 9 weeks flower this gives me 1.3GPW with an average dry weight of flower per plant of about 180g (6 oz).
I have my mother plant in a bubbler with a tapwater top-up float valve in a side tank syphoning into the bubbler under a CFL bulb. I often leave it alone for up to two weeks and while it needs a lot of TLC after so much LITFA, it lives and I can take clones from it. I have recently started a new mother as the old one had too much old growth on it.
For your system, I would advise to run a mother plant and clone area and then you can fully control the veg time. You can judge when to flower them based on the size of your rootball, which is the best way to judge it in a highly tuned system IMO.
You can still sprout seeds but put them in the veg room and clone them, then you do not have to take the initial time into account while you wait for the plant to go through puberty. This removes the problem of root growth during the time between sprouting and maturity.