The issue was with the IP.BIN file. That's where the metadata (among other things) is located. A few parts of the file seem to be incorrect (like the disc 1/2 thing) but a few parts seem fine and work perfectly on a burned CD or emulator, but don't play nice with the SD Card Builder for some reason.
Anyway, I made a new IP.BIN using IP.BIN Creator
, rebuilt the CDI, and now it works just fine with both SD Card Builder and GDEMU.
Just build a new IP.BIN, drop it in the data folder after you've populated it with the other files, and build the cdi. It should work perfectly now, on both real CDs and on the GDEMU / SD Card Builder. Here are the settings I used.
I tried editing the original IP.BIN using IP BIN 4 WIN (the program shown in the last screenshot) but unfortunately that didn't solve the problem. Only making a brand new file worked, so that's what I'm doing for now.
Unfortunately I'm still very new to the scene (it took a lot of reading and fiddling for me to figure out this much) so I wasn't able to figure out how to make a working GDI from the English translation. But at least the CDI is compatible with the SD Card Maker now. Here's a link to the ip.bin I made.
Hopefully this info helps someone!