Well, bruised roots should be much more prone to leeching loss. As I said, it would add another easily avoiable confounding factor for interpreting (negative) results.
Shouldn't really need nutrition in the medium if we're just growing to seedlings
Well, the energy stores are quite limited in small seeds. Cotyledons store the remnants left from growing roots and other tasks, and have limited photosynthetic ability. AFAIK, they lack laticifers. Teleologically, in case of nitrogen starvation, one would assume plants would not produce and/or degrade alkaloids for use in crucial protein biosynthesis. Teleology, as always, isn't necessarily trustworthy, but all in all, I doubt excluding nutrition would beget plants with the same alkaloidal profile as those raised in soil.
Why bother with the ethanol? I intend to germinate in vermiculite, wash away the vermiculite, then steep the seedlings in water like tea. I don't think washing away the vermiculite (if it's done quickly, in ice cold water,) will wash away any of the alkaloids.
My suggestion of ethanol is for combined disinfection and extraction, if grown in soil (a recommended course of action, even if the soil is sterilized).
Anyhow, if grown in vermiculite, why bother washing? Extract the seedlings with any vermiculite clinging to the roots. A simple sieve will suffice for separating it.
Doesn't anyone have access to that Phytochemistry article? Could help in estimating dose and time of harvest.