Concering the possibility for JMS to work with multiple hosting account, may be YES and may be NO.
All depends on the security of you hosting company.
If they have implemented a good security, theorically, the account can not access the files of another account.
If you want to test that, you could use the "hello world" procedure as described in the tutorial step 8
www.jms2win.com/tutorial and try create a link into a directory that is located into ANOTHER account. If it succeed, the answer will be YES. If it fail, the answer will be NO.
Up to you to test it.
Based on what I have read in the rochen forum , the case of domain.com, domain.net, ... is not a problem when it arrives to the same website. With JMS installed, you will have the possibiilty to create different website and not only a single website.
Something that will not works with JMS is the redirection. When you configure a hosting server with a redirection, you change the URL. This means that when JMS receive the hand, the URL is not the original URL and therefore probably will not display the website you want.
Based on what I have read, I suspect that different rochen account does not give the permission to access the files and folders of another account.
This is a feature required by JMS that need to share the files and folders on the disk for all the websites.
If you have a look in the video of the tutorial step 0 that present the concept, we quickly explain the usage of the Symbolic Link.
With the Symbolic Link, you create a brigde between different directories.
If you have no permission to create such links between account then this will be a problem.
You say that you would like to have separated website for security reason.
I repeat that the concept of JMS is to share the same joomla files and folders on the disk.
With the same PHP code, it is possible to create and access several DB connection in which you save the content of your website.
Therefore if you have different account, as JMS will require to have the Symbolic Link created to have access to the place where joomla is installed, then this mean that your different developper will also have access to those "common" files.