Since we already have such options for Sorting buttons.
Currently its (fixed) position can overlap with Quark's buttons.
Yes I can disable those, but what if I prefer Quark's?

Playing ATM9 0.3.5.

well, I am not so sure about preferring buttons from other mods. To be honest I feel like allowing sort buttons to be placed somewhere else was a mistake at least if different sort buttons would be shown in their place because those caused so much issues that they basically should never be displayed there / different sort should never work. With transfer buttons it's similar - in the past I added quark "compatibility" - it actually was all coded on my side to mimic what Quark did back then, with quark style buttons with an additional complexity of removing and adding buttons so actually more complicated than native feature - so that "Quark" feature worked well, but the main reason it was added was because Quark buttons were causing dupes / loss similar to what's happening with sort from other mods. So I don't really like the idea of quark doing the transfer and getting these reports again especially given that now there's native support.
I will consider this if there are some other buttons that can't be move that this would be competing with.

Well, my point is, for example, Soph's Transfer buttons will not show in Lootr's treasure chest, right? I can understand that sorting or transferring functionalities from other mods will not work properly with Soph's inventory, but I'm not only using Soph, like, sometimes such functionality is the only thing I can do for other inventories.

Is it possible to disable/hide buttons from other mods with this mod, though? Or should I open a new issue on their repo?

Other mods usually have configs to turn off buttons like this in specific screens. I am pretty sure that Quark does. Also it would be way way more difficult for me to add and maintain a compatibility that would remove their buttons from sophisticated screens just as a guide so if a mod doesn't have config like that you would want to ask them to add it.

I checked the config of Quark and found out that the config of "Easy Transferring" seems to only let you toggle the entire functionality. I don't found any settings that can toggle it for each interfaces.
So it seems like I should make a issue on their repo about this?

I am pretty sure it was hidden somewhere but yeah you would want to follow up with them / ask at their discord (I would think they have one)

closing this as it's really quark config question

In case you haven't found it or for future reference here Quark has these settings in quark-common.toml and specifically if this is setup in that config you will see the transfer buttons overlapping. "Allowed Screens" = ["net.p3pp3rf1y.sophisticatedstorage.client.gui.StorageScreen", "net.p3pp3rf1y.sophisticatedbackpacks.client.gui.BackpackScreen"]

Just removing these screen definitions from their config makes them go away.