Any ideas of speculation as to why this might be would be appreciated.
Essentially, the idea is to get across that the upper echelons of the Foundation have been flirting with the anomalous for a very, very long time. Including during the nine-year crackdown period.
Technically, most of the Factotum aren't any more anomalous than any Foundation researcher (they've almost all been affected by amnestics, remember? an anomalous technology). It's only a matter of degree.
Joshua's a more extreme example. Actually, from a certain perspective, he's worse than what's being done with Alpha-9. Alpha-9 is recruiting SCPs — SCPs which are already anomalous. But Joshua didn't start out anomalous. O5 Command made him anomalous. Because they can get away with that.
Part of the issue here is that with the proper access to materials in the mainstream Foundationverse, it is utterly trivial to become permanently anomalous, even if it's just in minor ways. And if you have access to practically infinite resources, as the O5 Council does… well, certain things become very tempting.
From that perspective, Alpha-9 is merely just one more step down that road…