Barring any Traefik tricks that allows me to accomplish what I'm after, I was thinking of going with your "third" option of just letting it use Cloudflare for everything but, I had to check with the experts first before just doing it.
I have some apps that complain or, in one case, flat out doesn't work if the cert is invalid. I've been working around it (sort of) but it would be nice to have it set up "correctly" for once. If routing all traffic through Cloudflare is the answer, so be it ¯_(ツ)_/¯
You're right, I'm using the cloudflare DNS challenge to get let's encrypt certs. I'm definitely hitting traefik. I'm testing by turning the Wi-Fi on my phone off/on and opening the page after. I get the same cert every time but it's not trusted when on Wi-Fi. This makes sense since it's the origin server cert which is meant to encrypt traffic between my server and cloudflare. To add more certainty, when Wi-Fi is on, a traceroute shows only one hop to my server and shows a bunch of hops when it's off.