Thanks for reaching out!
This sounds like persisting the variables works, but they are not actually taken into account in the booting process.
For a very high level test, can you try to follow the integration checklist at Integration checklist | Mender documentation? If you feel like it, there is also an automated version of it provided at meta-mender-community/meta-mender-validation/recipes-mender/bootloader-validation/bootloader-validation_0.1.bb at scarthgap · mendersoftware/meta-mender-community · GitHub, documented at Mender-validation: automatic integration checking.
Which MENDER_FEATURES are set in the build? Do you have a way to inspect the GRUB boot process to check if the Mender integration gets used correctly?
Greetz,
Josef