Apologies, when I said domain.com and domain.net, I meant ci.domain.net and ci.domain.com and that's what I'm trying to achieve. I just took a shortcut when writing it out.
I've removed the above mentioned middleware redirection and instead added this:
traefik.http.routers.jenkins.entrypoints = https
This is the output from running the curl command mentioned:
Moved to Gist because of Link posting Limit for New Accounts: Curl output · GitHub
So I took a look at my CloudFlare settings and realized both the main domain and the secondary ones for the A record had CloudFlare Proxy enabled (orange cloud thing). The secondary domains (.com / .net) where CNAMES of the .org domain as thus was doing:
.com / .net -> cloudflare proxy -> .org -> cloudflare proxy -> server ip / traefik
I believe this is what was causing issues with accessing the site using other ci.domain[dot]com/net and what caused all the confusion. This is embarrassing and I'm sorry for the confusion / complications.
Adjusting and refining the setup from your suggestions and advice was helpful neverless and helped me fixed my SSL / TLS implementation.
Thanks for the help!