When you play an Overlord as a Treasury, it correctly prompts you to put it back on top of your deck at end of turn.
However, it doesn't distinguish between actual Treasuries and Overlord as treasuries. I assume it orders them in the same order you played them, but that's an assumption.
In most circumstances, you would probably always choose to topdeck them, and the order isn't relevant, but there are definitely conditions where this is not the case.
===
To fix this, I'd recommend using the Overlord art instead of the Treasury art in the end of turn ordering menu.
Thanks for reporting this issue, Ryan!
Dominion online has sometimes a problem distinguishing cards to the user that are similar but need for whatever reason be treated differently. Your example is another instance of that, it seems. And I think that your suggestion is a very good one!