Are we even sure he is classified as D-Class? I don't remember anybody ever uttering the words "D-Class" in the cartoons. In "In The Pines" short we see multiple actual D-Class personnel being killed by 173, and they wear the exact same orange suits as Conner and his friends\fellow inmates, but does that mean that Conner and the other anomalous guys are D-Class?
After all, while I can imagine a few reasons for which you would design different suits, I can also see why they would just use the same suits. There are thousands and thousands of D-Class people, and only a few hundred humanoid SCPs - you may as well use the surplus clothing. It's not like they can complain.
All in all, the way I saw it is that Confinement simply takes place in a satirical, more lax version of the actual Foundation. Imagine LOLFoundation but without the 13 years old style of humour.
This version of the Foundation doesn't see fit to recluse all humanoid SCPs, and they instead prefer them to live together and socialize, probably to improve their mental health.
This also explains why Conner is referred to by name, and not by number. It's more humanizing that way.
I mean, of course this is a justification, the REAL reason is that the cartoon would be much more boring if it was about a dude that spends most of his time alone in a cell room with no human contact whatsoever, contemplating suicide not because he wants to die but because it's just a way like another to kill time.