Can't configure using Multisite under subdirectory with index.php under root

I’ve worked with both normal WP and Multisite WP installation for my clients which they were on the separated multiple installs – different domains, clients, folders, and database, these didn’t quite cause me a headache as it does to me now when it comes to my own current project installation. In the past, I used Multisite to achieve on multiple themes usage on one single site project.

I’m facing with problems on multiple updates of the WP core files, themes, and plugins – quite a time consuming and in need of some regular maintenance which some of my clients didn’t choose to pay for. Then having thought of setting up a single install on Multisite for my business to store and centralise all the subsites (on different client different domain and different theme) which most of them have nearly nothing in common except for some plugins. My existing problems and situation are:

My main company website is Non-WP site, having index.php resides under root and all related important files and folders dwelling under the root directory which are inevitable to change or move – my real core site – and highly preferable not to mix with any other alien files, WP for example. My WordPress MultiSite with the rest of their core files and else is under “/home” directory, called “MiniSite” based on WP platform has been already configured MultiSite/Network but having only one site (main WP site) working underneath it and trying the make the second site which belongs to my client to work along with this set-up but yet succeed in it.

define('WP_DEBUG', false);
define('WP_ALLOW_MULTISITE', true);
define('MULTISITE', true);
define('SUBDOMAIN_INSTALL', false);
$base = '/home/';
define('DOMAIN_CURRENT_SITE', 'mydomain.com');
define('PATH_CURRENT_SITE', '/home/');
define('SITE_ID_CURRENT_SITE', 1);
define('BLOG_ID_CURRENT_SITE', 1);

1. Having heard that it is achievable to set up Multisite under subdirectory while having index.php under root but highly not recommended as it surely will mess up with others in a long-run. Anyway as domain mapping tends to be considered and included within the WP roadmap on the next releases, I need to have this set-up to work avoiding my future time wasting and having all my clients in one place within the same network. Is it worth it, single install (one-for-all) and what have I done wrong?

2. Not sure whether it is a good practice to drag all my clients’ files and sites in sharing environment including tie-up my WP site with them when only some clients might share the same theme but many will have their own theme and plugins running. Should I stick with an old multiple installation (separate and individual core files but all under root) or single install (which is in subdirectory)?

3. Is it possible to have their own media files for each client kept under their own folder and categorized by month and year, ex. /home/wp-contents/blogs.dir/SITE1/2013/05, /home/wp-contents/uploads/SITE1/files/1/2013/08? If not, all the media files from different clients will get mixed up because they aren’t separated by network site name.

4. MultiSite concept is to share (by pulling up/referencing) the core files, themes, plugins, and others but almost less to none in having each physical files and folders on each client site stored under the core file, they are all stored well under their own database. Is my understanding in its concept correct?

5. Some themes might share the same plugins but on a different version, how could I cope with this, enabled all the same plugins on different versions?

6. Some says I could map http://www.mydomain.com/home/SITE1 to http://www.SITE1.com without Domain Mapping plugin, is that true? By the way, I did it but no success as it might because of the subdirectory.

Apologise for long read and thanks in advance for your help.