Hey! Both NesDS and SnemulDS work with regular boot (I've been using them regularly both through the flashcart menu and YSMenu) which surprised me even more. I don't exactly know the build of GBARunner2 I'm using right now, although I believe it is the last one in the wiki (don't really have any way of compiling one myself right now), but it is strange as I've tried every single build and found an old one that for some reason worked, but it seems like my R4 is blocking the dldi or something like that? I'm quite a newbie in this, but that's as far as I can tell. I'm fine with running it from YSMenu, I just wanted to check it out and I was satisfied that I actually got it to work.
OK. Thanks for testing. So the DLDI section is properly patched by loader (regular boot), because SnemulDS uses https://bitbucket.org/Coto88/gccnewlibnano_to_fsfat (gccnewlibnano_to_fsfat driver) (and all ToolchainGenericDS code). Also the sector size and cluster size relative offsets is held by Fatfs itself (so varying cluster sizes on different micro sd cards would iterate, for example, the first 512 byte FAT table and the upcoming data correctly).
And libfat does that as well so regular boot on your card is compatible.
Also, since DLDI Name is different depending on the loader, then the YSMenu DLDI driver could be compatible with the DLDI found in regular boot. (either by rebranding card name, or by very similar IC). This was common in the R4 clones using either DSTT or R4 DLDIs
Perhaps the _DLDI_startup payload (SD Init function) is different in the regular boot kernel, or the SD card commands (read/write) are poorly written in the regular boot DLDI?