Hi Charles!
As I showed in a video a while ago, you CAN absolutely use your HexPU. MIDI Guitar 2, Hexaphonic pickups and BOSS GP-10, is this the best setup ever? It also brings with it a great benefit in that it is possible to use the 6 channel alternative via the GP-10 for instance. But as far as pure audio goes, if you have a set of decent hum-free ordinary pickups on your Godin, I would probably use those instead. I haven’t experienced any particular superior properties with the Hex over my standard humbuckers. But it doesn’t hurt to try for yourself. If you get around to making a comparison, please drop a line as to what the result is. It is always interesting to hear about what works for different people.