No one has directly interacted with William and Logan other than Dolores. There is a host sent to bring her home... back to the farm. But the Delos control room conversation was about Dolores alone with no confirmation of other guests with her, and the instruction was to flag it with Behavioral to recover her and do a diagnostic, not "send a host to bring her back on loop" so it's not explicit that the events are related. If there is a single scene of the current control room actually acknowledging William and Logan, the theory is dead. That has't happened yet. It's a low bar.
No doubt MiB exist on the same timeframe as current Ford, Bernard, security guy, that chick, etc.
William, on the other hand, is weird.
Now I'm not part of the William=MiB camp. I'm still not convince there's any substantial evidence that can back this up.
But one thing I found strange is that I've yet seen William interact with any of the present day characters. Besides his friend, did he ever have any interaction with non-host? park employees?
Also, does anyone remember whether William have any interaction with Maeve? I'm asking this because based on her "memory" she was not always a prostitute.
So even if William is not MiB...I think it's still possible his scene are part of the past and not the present. But maybe he'll run into other character later.