Yeah, looks like you've got boring barnacles of some kind - they bore into the calcium carbonate skeleton of the coral under the coral's flesh (so you are right, they have drilled into the flesh), but they don't really cause any harm. As mentioned, they don't tend to last long in aquaria, so they shouldn't spread like coral boring spionid worm infestations have been known to. Neat find - not necessarily one you'd want to have with coral boring aspect, but still neat.
That said, the only time coral boring seems to actually be injurious to corals is with large infestations in the wild, where the infestations eventually weaken the coral's skeleton to the point where the strong waves or storms may break the coral apart (I've heard of this happening with large CBSW infestations, but not with coral boring barnacles which are super common in some reefs like Flower Garden Banks in the Gulf of Mexico), but the infestation itself doesn't actually seem to bother the corals).
It's possible it could keep the barnacles alive (it depends on the species of barnacle, the species of phytoplankton, and how much you dose), but it's unlikely. It's also extremely unlikely it would give you any headaches later, as you would need to be feeding the right kind of phyto in the right quantities (for the barnacle larvae reared in labs, this is typically 10^5 phyto cells per ml), and, even if you were doing that, barnacles go through two pelagic phases (nauplius larval stage and cypris larval stage) before settling, so they - like most other pelagic larvae in our tanks - would likely be eaten/removed by mechanical equipment/flushed out in a water change/etc. before settlement.
