Water based paints use the same (okay similar, just a different type of alcohol) vehicle as shellac based, just the resin base is different. If you eat the paint, you might have issue, but most attempt to avoid this. Toxicity concerns are way over rated, again, unless you're bathing in it. Some lab rats in California might develop issues when force fed doses of the stuff over several months, but . . .
Alkyd and acrylic primers are suitable, as are epoxies, which for the most part are lower in VOC's than the alkyds and certainly the modified versions of these. There are also waterborne epoxy primers that are easy to clean as well. Lastly, you'll need to tooth the surface just to get the paint to stick. You don't have to remove the texture, just a good scratching.