I did open a ticket for it but thought I would post here for comment:
MLAG synchronizes the LACP system-id of the secondary nodes ports with the LACP system-id of the primary node bonding interface that has the same MLAG id assigned to it.
Problem 1. If you reboot the primary node, the secondary node reverts its LACP system-IDs back to the chassis default. This causes an unnecessary forwarding flap/outage of 3-4 seconds (tested using 1sec LACP timers at least) when the primary node reboots. The same flap occurs when the primary node comes back, restoring MLAG peering and the secondary resets its LACP system-IDs to match the primary peer.
Problem 2. Somewhat related as it helps get you to a solution. You run different LACP system-IDs on every bonding port by default. This is technically wrong. The LACP system-ID should be the same for the entire chassis (And as such, the same for all MLAG peers). It bears no relevance to the underlying MAC address of the physical port. IT is used only for signalling. Only the LACP port ID should differ between different bonds.
Problem 3. Similar to problem 1, when the primary node reboots, the RSTP bridge ID reverts back to default. In an MCLAG environment with RSTP, both peers should always carry the same bridge ID at all times because they are by the very definition of MCLAG, the same physical port/device.
Solution: When the MLAG pair comes up for the first time and one device becomes primary, the MAC should be synchronized to the secondary peer and become immutable. This way, if the primary node reboots for an upgrade, the network never experiences any major re-convergence ( From both RSTP and LACP point of view). The port-ID of the primary device should be the MLAG ID. The port-ID of the secondary device should be the MLAG ID Plus some fixed value.. say.. Add 128 for each port on the local switch, add 1024 for being a secondary device. This insures that all LACP port IDs are unique across all ports in the bundle (Even across different switches). The LACP system ID would be the same across all devices.. All of these will be immutable. The LACP port KEY should generally just be the MLAG ID and be the same across both devices.
Enhanced solution (More preferred for those keen on MLAG): Allow a static LACP system ID to be set and a static RSTP bridge ID to be set. The RSTP bridge ID should not affect the MAC address of the actual bridge itself, each devices MAC should be unique for L3 purposes. Also let the user specify which device is node0 and which device is node1.
In both solutions, only MLAG bonds should be affected. the bond used for the ICL port and other non-MLAG bonds should follow traditional logic.
IT should also be noted that I observed inconsistent behavior with the RSTP ID and bridge mac of the secondary when the primary is rebooted if you dont have a static admin-mac set on the bridge.