I agree. An MC controller could keep track of the Quarter Notes like any other looper or sequencer, and should do so based on the presence of MIDI Start if the feature ever proceeds. Execution of Start could happen when the user has placed a Start command on an MC switch, or when received externally. Whether received externally or sent from within the MC Controller, it stands to reason that every device in the MIDI chain that’s also listening for the Start command will all have their count aligned. It’s been like that for decades.
Here’s more background.
Clock pulses merely keep devices from drifting away at their own rate, which happens over time to every device even when they are set to the same BPM internally. Clock isn’t really meant to do any more than that, which is why Clock data conveys no details such as quarter note markers or even BPM (devices don’t even know what the BPM a clock is sending at without calculating it themselves after sampling a few of the pulses).
Along with Clock, the other basic part to obtaining sync is MIDI Start (and Stop). When devices receive a Start command, they wait until the next Clock Pulse to reset their counts and begin doing whatever it is they’ve been programmed to do. This is what insures that every device considers the same pulse as the 1st one, even if Clock has already been running for a time. That also means if Clock is not already running when a Start command is received, the device should consider itself in a pending state. Devices are not supposed to simply execute start internally as fast as they can when the message is received. (some manufacturers have gotten this wrong, but most get it right).
You also see some devices implement a Resync feature to allow users direct control over realigning the count and restarting whatever it is the device does. Resync isn’t a MIDI standard command itself, it’s a batch of commands that effect an outcome.
Stop, of course, is the purview of the MIDI Stop command. The clock can even keep running when Stop is received; Stop isn’t actually a command to Stop the Clock, just as Start isn’t actually a command to Start the Clock. That gets a little muddied because many devices tightly couple Start/Stop with starting and stopping the Clock, which I’m not even saying is a problem, it makes sense in a lot of scenarios. I’m just saying that it leaves an impression that Start/Stop is specifically about controlling the presence of Clock, when it’s not.
What you are saying about Clock not being received for X ms for a device to consider things have Stopped is right on. If a device is in a state where it is dependent on Clock pulses, then the absence of Clock pulses gets treated as an implied Stop, even if no MIDI Stop command was received. It’s not uncommon for devices to have that kind of behavior in their programming.
I’ll just finish with this. In the implementation that I see, a general purpose MIDI Controller such as an MC can both implement its own count for cueing commands to a rhythmic interval, or it can rely on triggers/markers coming in externally for cueing (presumably the external device is being relied upon for the rhythmic context in that case). These aren’t mutually exclusive choices. You can always do one or the other or both and introduce them in separate releases. One choice (counting internally) depends on Clock and internal resources to keep track of that rhythmic context. The other choice (responding to triggers) doesn’t require anything other than putting commands in a pending state and waiting for the trigger to come in.