The Catalyst 9300-M and the MS390 are indeed built on the same Catalyst 9300 platform. However, there are differences in their software and how they operate.
The MS390, as you mentioned, runs the Meraki OS in a Kernel-based Virtual Machine (KVM) on IOS-XE. This was indeed the cause of the long boot time and some of the issues with the platform.
As for the Catalyst 9300-M, it's not explicitly stated whether it operates differently from the MS390 in terms of its OS. However, it's important to note that the Catalyst 9300-M is part of the Catalyst family, which is known for its robustness and reliability.
In terms of hardware, both the MS390 and the Catalyst 9300-M offer similar features, such as high-density stacking bandwidth, flexible uplink offerings, and high multigigabit ports.
However, without specific information on the Catalyst 9300-M's software operation, it's difficult to provide a definitive answer. I would recommend reaching out to Cisco or Meraki directly for more detailed information on the differences between these two platforms.
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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