Hah, I've not played much of Factorio 2.0 and haven't tried the quality myself yet, spending much more time on mods updating... 😒
Well, this is not a bug nor is intended, it's just how the mod worked all the long time – depots have only one output stack, the drones put there usual ore items, and there is no room to place ore stacks with other quality, nor code to produce it.
AFAIK, quality results are made with quality modules only and don't appear without them. Depots have no modules slots at the moment, so, I also will need to make code to handle modules 🤔
All these things are quite fixable, but it will require much time and motivation from me. Probably, I'll make it one day, but there are no time expectations for now.
In case someone have Lua scripting, Factorio modding skills and would like to participate, collaborate on this open source project, reach me on Discord.