You need to boot your slot-2 device in NDS mode since GBA mode does not have access to any of the DS related hardware like slot-1.
In DS mode, homebrew typically use NDS file extension. gba file extension is used for GBA homebrew executed in GBA mode.
The better option is to simply boot from your slot-1 card and run the slot-2 version of the dumper homebrew of your choice from the slot 1 flashcart. It does not need to be executed from the Supercard device in slot-2 for it to see it. You could still keep your dumper homebrew file on the storage of your slot-2 if your slot-1 cart's OS has the ability to browse and launch files from it. (my R4 with WoodR4 firmware for example supports this)
You "might" need to manually DLDI patch it to use the Supercard in Slot-2, But as I recall the slot-2 dumpers out there that I've used shouldn't need this and should automatically recognize what ever you got on slot 2. I used to have the Max Media Dock and I do recall DLDI patching the slot-2 dumper specifically for that device. But the more mainstream EZ 3in1 and maybe the supercard may have built-in support. Especially if it's the Wood R4 dumper.
Boot your slot-2 dumper from slot-1 cart. When it is ready to dump a game, remove slot-1 cart and replace it with the game you are dumping. The slot-2 dumpers I am used to using run from internal ram once loaded, so it's safe to remove the slot-1 cartridge they were booted from as long as you do it at the correct time as indicated by the menu prompts in the dumper you are using.
If your dumper supports soft resetting back to your flashcart menu, be sure to reinsert your flashcart before doing so.