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Our school's club website is at example.com. This is site is blocked on our school network because the domain is not in the list of school resources. The school offered to give us a subdomain of their website at example.school.edu, however I would still like to retain our main site as it is just a much more desirable and concise domain. I have tried using https://wordpress.org/plugins/multiple-domain-mapping-on-single-site/ to clone the site, however it ends up requiring the client to enable mixed content. How can I fix this issue

This is what REST API is for. You can set up a site on any domain, on any host, and pull content from a WordPress site. You can set up a WordPress website and connect to your school’s WordPress website and pull content from it. This is referred to as “Headless WordPress”. Google or YouTube it.
I do not think it will be worth your effort and introduces potential issues. I would just take the school up on their offer and use their subdomain, and if you want forward your vanity domain to it.
Also, your school IT may restrict what capabilities you can do on their webservers. To do this you’d need to setup a domain alias, and they may not allow that or give you sufficient access to.
Even if you could, it would cause confusion for users who may try to access your vanity domain on the school network, for example, and get blocked.
If you really want to try, though, one option that you could explore, but it’s a bit more technical, is using a reverse proxy. This could be setup for cheap / free using CloudFlare workers. You’ll need to use CloudFlare DNS for this. It could also be done with an NGINX web server, but CF Workers are free for 100,000 requests per day. This would get around issues with school IT and web server configuration / access.
I believe there are domain mapping plugins that do this
In my opinion just have the main domain forward to the school subdomain. Then later on you could export it to the main domain. Or just have your school approve your domain name for the club.
I wouldn’t fix this problem with programming first. I’d solve it in the above ways. And if they aren’t possible or not desired, then I’d worry about cloning websites.
Just fyi the internet doesn’t like duplicate websites or content. Depending on your use case it might be a bad idea to have a duplicate site.
Just create a backup using all in one migration and restore it in the new domain. This will literally take 1 hour, only that you will have two sites.
Yes, you will have to request CNAME update in DNS records from subdomain authority.