How to properly setup SSL with Apache2 and multiple Docker containers?

Yes, this seems like a good configuration. I don't see any obvious problems, except the one in your question 3.

The only problem with letting the http://*.domain.com:6xxx connection through is that it's HTTP, not HTTPS. To prevent that you can redirect those connections too:

RewriteCond %{HTTP_HOST} ^(.*)\.domain\.com$
RewriteCond %{HTTPS} off
RewriteRule (.*) https://%1.domain.com$1