Not faulty, the issue is that meta-mender provides a never version of U-Boot which also changes how the recipe is build and the bbappend in meta-imx is not applicable anymore.
Creating another u-boot-tools_%.bbappend
as following solves it (instead of using bbmask):
do_compile() {
oe_runmake -C ${S} sandbox_defconfig O=${B}
for config in ${SED_CONFIG_DISABLE}; do
sed -i -e "s/$config=.*/# $config is not set/" ${B}/.config
done
oe_runmake -C ${S} cross_tools NO_SDL=1 O=${B}
}