I could make two profiles, but they would both have to use the 8 bit target that ColorMunki sends to the driver. I don't if there is a way of getting a 16 bit target file out of ColorMunki.
You don't even have to make two profiles. Save both data files and examine them in a text editor or plot the deltaE in something like ColorThink.
The data is either identical (within the slight variations of instrument measurements) or its not. I'll but dollars to doughnuts its the same in either case of the bit depth used.
In the case of ColorMunki, its sending 8-bit data. Now the Canon export module, that will send out more than 8 bits of data if so set. But I'll bet after you measure them both ways, you'll get the same data (again note that if you measure a target twice, you'll never get a zero deltaE between the two values. They should average well below 0.1 on a decent device).