I agree that measure numbers cannot increment naturally across time signature changes, since the MIDI clock standard does not permit it. The standard seems to say that the slave’s SPP must remain equal to the master’s, irrespective of meter.
But I don’t think Cantabile correctly preserves the SPP at meter changes. Here’s why: Even in songs where the master’s meter never changes (e.g., remains 4/4 throughout), if I change Cantabile’s meter to the master’s meter (e.g., change from 6/8 to 4/4) partway into the song, my downbeats do not match the master’s throughout the remainder of the song. If Cantabile’s SPP matched the master’s SPP, the downbeats should align, right?