Thanks for your message and... Welcome.
A1: Customization in Phraseanet is limited to the login page, registration page, password recovery page, Terms of use page and oAuth authentication page.
To customize those pages you must deal with LESS and TWIG. I try do write a page for this in the manual
docs.phraseanet.com later this week.
For more customization, our product Parade has to be considered.
A2: We try to keep compatibility whenever possible.
A3: Yes, it is possible. From the Install directory the Console command is bin/console system:export [/path/to/export/directory]
Various options are supported. Type bin/console system:export --help for more information.