First, the files look identical. Please show the diff of them (if they do differ).
Second, the value of GRUB_ENABLE_BLSCFG is read, but not apparently written/changed in 10_linux.
Third, the /etc/default/grub is used by grub2-mkconfig (which uses the /etc/grub.d/ scripts to do the work). The work is to create grub.cfg. Update of packages does not call grub2-mkconfig, AFAIK. Install of new kernel does probably use grubby to modify the grub.cfg (if BLS is not used).