JSON is way easier to work with for "machines". The Caddyfile is a user-facing layer on top of that. The Caddyfile doesn't map as nicely to something usable at runtime. That was the entire point of the Caddy v2 rewrite; the v1 Caddyfile was inflexible and was turning into spaghetti.

Like Matt said, I don't understand the problem here. Just use the Caddyfile. What problem do you have with it specifically? If there's a feature you're missing or aren't sure how to use, open an issue or ask for help on the forums.