If the real question is: can you manage multiple domain names from a single WordPress multisite network, then the answer is yes. But you’ve over-specified your restrictions such that the question is no longer answerable.
A WordPress multisite network – either as a subdomain (site1.example.com) or subdirectory (example.com/site1) install will allow you to manage core, Themes, Plugins and users, across the network and per-site. The Domain Mapping Plugin will allow those sites to be accessed as e.g. site1.com, regardless of network type (subdomain or subdirectory).
But, taking your points one-by-one:
- Can I create a Network within the MultiSite (WP v3.7.1 to-date) configuration but NOT based upon subdirectories or sub-domain basis as
each site has its own theme, plugin, and domain name: Site1.com,
Site2.com, Site3.com for example?
A WordPress multisite network, whether installed as subdomain or subdirectory, combined with domain mapping, accomplishes this.
- The main site will not be under “root” directory but dwell within /subfolder instead, if the question#1 above is achievable, all the
rest of the sites will be within /subfolder/wp-contents/theme << each
theme per site in different folders, is it possible?
You cannot put “sites” inside of wp-content. That’s not what wp-content is for.
- Is this the good solution in terms of a security issue as it seems all the sites are under one roof?
This is a subjective question, the answer for which depends entirely upon your specific needs. But multisite network installs do facilitate site maintenance/update.
- Each client, each site, each domain has their own login screen and could be able to claim their rights over their site only, what if they
do have multiple users who need a log-in, will it mess up with another
client site including my own main site as well?
With domain mapping, users would login via site1.com/wp-admin. With a multisite network, you can manager users across the network, and can add users to one or many network sites.
- Don’t quite see the whole picture how InfiniteWP plugin could help me either to minimise the WP core installation or centralise all the
sites in one place?
No opinion on InfiniteWP, and Plugin recommendations are off-topic.