How can I remap the left keypad keys of a Kinesis Freestyle keyboard on macOS Sierra?
Unfortunately the answer linking to the "auto-repeater" software would have the unwanted result you mentioned of trying to remap the basic ⌘-arrow keys.

As I'm sure you know by now it's not possible to remap the keys on the Kinesis Freestyle keyboard as it's not programmable.

They answer this question in their FAQ on their website:
https://www.kinesis-ergo.com/support/technical-support/faqs-freestyle-keyboard/

Disclaimer, I know this is 7 months old at this time but it's a top Google result and didn't have a proper answer