It seems that the code that controls MTU on an interface was suddenly placed in the wrong place which made it depend on IPv6 global settings.
https://github.com/vyos/vyos-1x/blob/bafb1973d906707cb571385e994a949d0d90b645/python/vyos/ifconfig/interface.py#L1501-L1531
Most likely, MTU-related code should be outside of if sysctl_read('net.ipv6.conf.all.disable_ipv6') == '0'.