pfSense

Minimal reproducible configuration:
round-robin LAGG pair assigned as the WAN interface with either an MTU of 1500 or no MTU set.
a GIF interface (he.net tunnel used for testing) assigned as OPT1 with an MTU of 1480 set.

System:
Intel i3 8100,
16GB RAM,
Chelsio T422-CR 2x10Gb/2x1Gb NIC,
2x Intel I210AT 1Gb NIC

(Also tested on an older i5 2500-based system with 4x Intel Pro/1000 PT NICs)

Issue:
In the stated configuration, the MTU assigned to OPT1 is applied to the WAN interface on each reboot according to Status > Interfaces and ifconfig.

This occurs with both Intel and Chelsio NICs. I have not tested with other brands.

This occurs whether the MTU of the parent interface is specifically set to 1500 or left at the default value.
Once the issue manifests, any MTU setting for the WAN interface is ignored.

Clearing the problem involves removing the MTU setting from the GIF interface before setting the WAN interface's MTU to a temporary value.
The WAN interface's MTU can then be returned to 1500 (or the default setting) and the MTU limit on the GIF interface restored.
The correct MTU remains on the WAN interface until the next reboot.

The problem does not occur when the NIC is set to a single, non-aggregated interface.