Rather than post this as a bunch of comments, I’m going to make this an answer.
Your requirements/questions:
to Have a Super admin that has access across all wp sites.
That’s a hallmark of Multisite.
to use both, subdomains and subfolders, in the chosen setup (see example above).
You can accomplish this with something like the Multi Network plugin, as I understand it.
to know which is better for SEO?
Someone else would have to answer that; I’m not an SEO expert.
for all sites to share media folder
This isn’t something that WordPress Multisite does, so you’d need to find a plugin (or build one / hire someone to build one) to do this. You’d be in the same boat if you use a group of single-site installations, too.
for all sites to share the main template file
You can use the same theme on all the sites in a Multisite network; you can even set a default theme for new sites in the network using the WP_DEFAULT_THEME constant in wp-config.php.
each site to have its own database
Multisite separates sites into their own tables in the database, with a common table for the users (all users are able to be added to any of the sites). eg, if you’re using the default wp_ prefix in your database, then for these sites:
Maindotcom (WP SITE)
/about
/department1 (WP SUBSITE)
/department2 (WP SUBSITE)
department3.maindotcom (WP SUBSITE)
/contact
/blog
… your database would be something like this:
// tables for maindotcom
wp_posts
wp_postmeta
wp_options
...
// tables for maindotcom/department1
wp_2_posts
wp_2_postmeta
wp_2_options
...
…and so forth.