Unfortunately I'm no expert in the field of straw building. I do, however, know a thing or eight about fungi.
If you're sure that the clay straw is dry enough -throughout-, there
should be no problem of molds even if you plaster over it. Funguses can only thrive if the substrate that they grow on is sufficiently moist.
Superficial mold damage in basements for example are fixed by thoroughly removing the moisture from the air and damaged areas. After that, the moldy spots can be scraped off (I can't stress the need for a decent respirator enough for this procedure) if paint is to be applied. But even if you leave the mold as is after drying, it won't be able to grow if the humidity of air/ substrate is low enough.
Since you already sprayed your claystraw with a fungicide (borax), I don't really see why you couldn't plaster right over the mold. As long as the plaster sticks well enough. Mold doesn't produce
fruit bodies, but instead generates spores straight from the mycelium. That could bring out a problem in the adhesion of the plaster.
One other thing that comes to mind, is that earthen plaster is probably a better alternative than cement stucco for you. I base this hypothesis solely on the fact that cement breathes much more poorly than clay. -And is required to stay wet for as long as the cement cures. The humidity from the cement might end up getting trapped in to the wall for a longer time, resulting in rehyrdation of the straw. But again, even this should not pose a big threat if the borax was applied carefully.
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