A different address-family is not a problem, just configure it as every other configuration. Both that’s not really a NAT46, or any NAT for that matter, haproxy works with sockets, and they can be of different address-families.
Depending on your actual use-case, haproxy may or may not be the right tool for the job. If you want to place a dual-stacked reverse proxy in front of your backend server that are v6 only, then yes, haproxy will do that just fine.
But if you need a forward proxy, then there are probably better tools for the job.