Hi
I think you`ll be fine with perlite.
With my hydroton flood and drain bed big seeds can be literally just be thrown in. I put small seeds on a small piece of tissue which helps stop them falling too far into the bed. It doesn`t cause the roots any problems afterwards as it tends to dissolve after a while.
With perlite i`d just plant the seeds fairly shallow and let the wicking effect of the perlite keep them moist rather than soaking them and risk washing them deeper into the bed.
Once they germinate the roots will go looking for water, i find plants grow better if they have to work a bit to survive :)

Yea this would work but my concern is that you may be wasting a lot of time and/or artificial light (a.k.a money) by germinating seeds directly in the system. If you use starter plugs of some kind you can let a plant grow for two or three weeks or more before transplanting it into the system - just stick them in under the light where you have the space - while other plants are growing in the system. That way your light is growing full term plants while you start seeds for the next time, and your garden can have new plants ready to go when the old ones are done.

If your running with artificial light that may be the case but some do use hydroponics without :)

This thread is all about low cost starter plug alternatives.
With starter plugs you system will not have holes where seeds didn't sprout plus you can pick the healthiest from the batch to stick in your system.
Just my take on it of course.

Yea believe me I wish my house was aligned with the sun, or I wish I had a greenhouse, to take advantage of natural light. I am however going to do some outdoor hydro stuff as soon as I can get it set up. It won't be a controlled environment so I'll still have to stick with the seasons, but you pretty much can do stuff year-round in central florida anyways.

My comment was directed mostly at someone who is or must use artificial light.