Hi Jet,
Due to the inevitable inherent limitations of many vendors midi implementations I've finally decided to invest into a BomeBox and Bome Midi Translator Pro for flexible workarounds for my custom use cases. If you can't wait for the vendor to fix it, you might be able to find a workaround with the BomeBox Swiss Army Knife.
With Bome you could "potentially" transform or "remap" the PAD messages coming out of the MKII into any number of midi messages, computer keyboard/mouse commands to switch a midi channel on application running on your computer host. You will need to consider that some basic programming will be necessary to build the script to do what you want. Bome has great support and they are very helpful .
You could in your script look have the BomeBox look for the Pad1 midi message coming out on channel x. When the script sees the Pad ID, it can start transforming all the midi channels coming out of the Bome Box to any channel you like. You'd need to have a simple test for each Pad ID #. When Pad 3 is pressed the Bome box can rewrite the midi channel number you like. The devil is in the details. But ya, you could do it externally.
Look into the Bome Forum and leave a question about your use case to see what they can do for you. Good Luck. BTW, I own a the 61Mk2 also.