You are suggesting me to install SFFS in both PC then create a group of profiles in each of them which synchronize with the same target (in the Pendrive). Am I entitle to install two copies of SFFS if I only purchase a license (Pro edition for Windows)?
Yes, and it can be used on one computer at the same time.
You may be able to combine a lot of the profiles into one by specifying the common parent folder, such as C:\Program Files, and selecting the subfolders in that profile. It's not easy to have an application-specific file mask then, but maybe copying a few files more than actually needed is better than having lots of profiles. You can however type paths with masks in the Inclusion Masks field, such as \Program 1\*.PRG. If you want to do that, you need to select the subfolders of Program Files and also type each folder with mask in the masks field.
Is it possible to/ how do I create a shortcut so that I can click it to execute backup of all/some of these N groups of profiles?
Yes, for example the command line C:\Program Files\SuperFlexibleSynchronizer.exe /RUNX=Group* starts all profiles whose name starts with Group. But use C:\Program Files (x86) on a 64-bit Windows. You can also use multiple /RUNX="Profile Name" parameters. See also
http://www.superflexible.com/docprofi.htm.
1. Is there no way for me to control compression ratio if I backup to zip file(s)?
No, but you can exclude file types from being zipped on the Program Settings dialog.
2. For Zip Package, if I don't tick the option "Use Profile name for Zip file name", then what name will the zip file be?
I think it is named Backup + timestamp etc. But you cannot use Zip packages for your purpose. All files must be zipped individually so that they can be seen as separate items on the pen drive. Otherwise you can't do a two-way sync. Zip Packages are one way only.
Also, the Versioning options apply only to individually zipped files. As opposed to Zip Packages, which will just pile up indefinitely.