"site zero", was likely the Pleiades.
In FFE lore Mic Turner discovered that the Pleiades was the Thargoid Forward Base, and if you look at this map https://map.canonn.technology/all/ filter for Thargoid Bases, you'll see most "inactive" ones (the most damaged ones) are the areas facing the bubble. That seems to be a good indication that those ones were infected and damaged in a wave originating at the closest point to the bubble, and my guess would be that INRA just infected as many bases as they could along that front and the infection spread back from there.
the INRA logs show they were making a lot of the Mycoid, but hyperdrive tech back then was slow, so they likely just hit as many bases as they could easily reach. Comparable to the USA detonating the atomic bombs on Japan, they didn't need to destroy it all, the Japanese leaders knew they couldn't defend against atomics and had no real choice but to surrender.
I assume that the Thargoids retreated so as not to get infected once they realised what was happening.
I don't think the Flower ships are Thargoids specifically, I think they're basically space-based scavenger drones (and maybe test beds to see if we've made more mycoid, since I assume they're returning because they've developed a resistance to it). They're checking over the area, collecting resources, scanning everything and taking all that info back... somewhere!
As to their current whereabouts; Again, in FFE the Thargoid home planet was located a long way off and the general direction seemed to be what we now call the Col70 sector, and ofc the signal from the probes points to a system in the Col70 sector, so best guess currently is that the reason that sector is locked is that it's the Thargoid home systems. We know the Mycoid attacked their ships, so it's possible the bulk of the Thargoid population quarantined themselves to prevent the mycoid spreading.
The Mycoid was deployed in Miacke in F:FE I bellive. That system does not exist in elite dangerous. Unless it does but has been renamed.