Hi aJan,
May I ask whether are you trying to use HPS or Nios for your design, as first phase it is HPS based, then 2nd phase you're using Nios Shell to run the quartus file generation?
If you're using HPS, perhaps this guide will help (it is based on 24.1 since you're using 24.05)
https://altera-fpga.github.io/rel-24.1/embedded-designs/agilex-5/e-series/premium/gsrd/ug-gsrd-agx5e-premium/#build-sd-card-boot-binaries
I suspect is because you're using the precompiled version of u-boot-spl.dtb.hex thus you're seeing some boot failures here, as any hardware mismatch between the precompiled configuration based on precompiled design vs the design that you have will result in error as it needs to matched correctly
Could you try recompile the u-boot-spl-dtb.hex first following the guide on top, its compiled as part of yocto build and then proceed with the rest of the sequence per the guide. May I know your Quartus pro version as well? Usually we will advise to use the matching Quartus version with the release baseline.
Thanks
Kian