So I have a GDEMU and a disc system. I can't help you with your problem just yet, because I'm using PSO ToSEc rips with no patching at all. I don't own a cd burner either, so I have never used a patching disc with my disc-based system with PSO.
I don't use SD Maker to make cards for my GDEMU I use my mac and just drop the files on one at a time. ie whole games at a time. This seems to work better for space management on the SD card. I also use only 16 and 32 GB cards and just make collections of games. I bought a handful of cards from the store at the time to test. I found a cheap brand Centon and Kingston worked best for me.
I will try messing around with some of the patching disc isos this week. I'm not super clear on why we need to use these patching discs anymore with the dream pi setup. If anyone would care to explain in a nice fashion that would be appreciated.
I never used boot discs with my DC in the 2000s and frankly, at the time I moved on to playing games on other consoles after DC's demise. I always missed PSO and the fun I had there. I even kept most of my DC games at that time until now. I guess I missed out on the fun everyone was having patching to get new servers up and running.