Sites are increasingly using Certificate Pinning mechanisms which can break HTTPS access when using a Man-In-The-Middle proxy. Transparent proxies never worked well with HTTPS, and are becoming increasing broken. You can block traffic on port 443 except from the proxy. This will prevent unproxied requests. It is possible to use iptables to redirect unencryped (HTTP) requests to a transparent proxy.
I would suggest publishing a "wpad.dat" file directing Internet bound traffic to your proxy. Many clients use automatic proxy discovery. This will enable clients to connect to the proxy in using non-transparent mechanisms, that will allow HTTPS connections.