It turned out that the U-boot configuration fails only if I use the eMMC template instead of the SD card template from meta-mender-community/mender-variscite/templates to create my local.conf file. With the SD-card template, the U-boot patching didn’t yield any errors, and I was able to build a working Thud-based SD card image.
In the meantime, I’ve come across a topic on this matter:
How to write DART-6UL image to eMMC
I don’t really understand how the original poster got the eMMC booting to work, but it seems that he may have used a local.conf initially tailored to SD-card booting, with a few changes made to the MENDER_STORAGE_DEVICE and MENDER_STORAGE_TOTAL_SIZE_MB variables to boot from eMMC.
Does this procedure make sense, or am I missing out something?