I'm not confident about this, I've seen and heard many scenarios where MST was an issue.
MST Case
MSTs (IEEE 802.1s) combine the best aspects from both the PVST+ and the 802.1q. The idea is that several VLANs can be mapped to a reduced number of spanning tree instances because most networks do not need more than a few logical topologies. In the topology described in the first diagram, there are only two different final logical topologies, so only two spanning tree instances are really necessary. There is no need to run 1000 instances. If you map half of the 1000 VLANs to a different spanning tree instance, as shown in this diagram, these statements are true:
Map Half of the 1000 VLANs to a Different Spanning Tree Instance
From a technical standpoint, MST is the best solution. From an end-user perspective, the main drawbacks associated with a migration to MST are:
The protocol is more complex than the usual spanning tree and requires additional training of the staff.
Interaction with legacy bridges can be a challenge. For more information refer, to the Interaction Between MST Regions and the Outside World section of this document.
MST Region
As previously mentioned, the main enhancement introduced by MST is that several VLANs can be mapped to a single spanning tree instance. This raises the problem of how to determine which VLAN is to be associated with which instance. More precisely, how to tag BPDUs so that the receiving devices can identify the instances and the VLANs to which each device applies.
The issue is irrelevant in the case of the 802.1q standard, where all instances are mapped to a unique instance. In the PVST+ implementation, the association is:
The Cisco MISTP sent a BPDU for each instance, with a list of VLANs that the BPDU was responsible for, in order to solve this problem. If by error, two switches were not configured correctly and had a different range of VLANs associated to the same instance, it was difficult for the protocol to recover properly from this situation.
The IEEE 802.1s committee adopted a much easier and simpler approach that introduced MST regions. Think of a region as the equivalent of Border Gateway Protocol (BGP) Autonomous Systems, which is a group of switches placed under a common administration.
I am not a Cisco Meraki employee. My suggestions are based on documentation of Meraki best practices and day-to-day experience.
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