Hello,
Yes, you should be able to do that.
Certificates aren't too concerned with what port you are using, so moving between 2222 and 443 shouldn't create any popups as long as the hostname is the same (if you are using the same cert/key for both da and apache), and the CA Root Certificate is installed in both apache and DA.
You can use different certificates for both apache and da and not get any popups if the domain in the certificates match the domain in your webbrowser whever you are. Basically, if you install valid certificates and login to DA/Apache ssl with matching domains, you shouldn't get a popup.
John