Nice to know that the new Canoe patch format is working with the update. I very highly doubt there are any issues as they are extremely similar. There are things that keep liberties extended from being compatible with everything and that's why there are two BPS patches, but there should not be anything that would break Sluffy's patch.
It's working, but sluffy's .bps canoe patch that you converted to an .ips patch for some reason reverts the sky/dark menu icons back to lightning/shadow while using your Bugfix+SkyDark and Name Liberties patch.
Both the .ips and .bps canoe patches change your game from a ExHiROM to ExLoROM + S-DD1 so it plays in Canoe, just that issue with the menu icons when using your patch with the .ips Canoe patch you uploaded.