The MTU of the physical interface will always need to be larger than the MTU of any L3 logical sub-interfaces. That's because when sending an IP packet from a sub-interface the physical port will also need to append a VLAN tag (4 bytes) to the ethernet header so that traffic from each sub-interface can be differentiated. Now, because the VLAN-tag is in the ethernet header and not the IP header, it isn't counted in the IP MTU of the sub-interface, but it is counted in the physical MTU of the parent interface.
At least that's how it works in Junos OS. It's been a long time since I've wrestled with IOS, but do I recall the way MTU is calculated being different and not particularly intuitive by comparison.
Could this cause issues with other routers or implementations? Have you encountered any implementation where the sub-interface MTU size changes when the physical interface MTU is modified?
In Junos OS if the sub-interface MTU size is not configured, it will change in lockstep with the physical interface e.g.: if you increase the physical port mtu by 10 bytes, the mtu of the logical sub-interface will increase by 10 bytes (but still always be 4 bytes less than the physical interface).
If however, you configure the IP MTU of the sub-interface and then increase the MTU of the interface, it will remain as per your setting, which is a sensible default (otherwise you'd be overriding configuration which is not good).
If you try to lower the interface MTU or raise the sub-interface MTU to within 4 bytes of the other, Junos OS will throw a commit error and not allow you to proceed.
The only reason to ever mess with the IP MTU in an OSPF scenario is if you have mis-matched interfaces - ADSL WAN circuits with PPPoEoA at one end (MTU 1492) talking to routers with Ethernet (MTU 1500) on the other end is a classic.
In this scenario, Cisco has a knob ip ospf mtu-ignore which will allow OSPF to form an adjacency regardless of the differences. You will then need to adjust segment sizes of TCP traffic transiting the link with ip tcp adjust-mss 1452.