I ended up having to switch to ACF for a specific project because of this particular limitation. I'm using custom fields quite a bit on the Product and Order post types.
My client is getting a couple of thousand orders per day, and we need HPOS to be enabled. I was pretty far along in the project when I realized MetaBox doesn't support HPOS.
I had to pivot, which sucked since I had to manually recreate all the fields as there is no MB to ACF import/export option available in ACF.
MetaBox should be on top of this feature more than ACF, especially since it already has native support for custom tables.
HPOS support needs priority. This represents a significant shift for WooCommerce; not supporting it means MetaBox only partially works with Woo.