Hi. I do understand that you may expect something different based on what you are used to, but only because an addon is designed to do something in certain ways does not mean that's a bad product. The addon does what it was suppose to do, and of course it has a few limitation imposed by the bookmarking system that is used for storing data. The whole idea of the addon is to have session stores as bookmarks. Because of this, there are some limitation that you have noticed.
Yes - sadly each window is treated as a sort of separated session when saved into bookmarks. You can either save windows one by one or save all of them at the same time. From my own experience there is clearly not a best description of what "session" means for each one of us. For some, different windows should be treated as separated contexts while for others consider all windows to be part of the same session. No matter what decision I take, if I don't have good support for implementing the features required into the bookmarking system for sure there will be missing features.
I clearly do not expect the addon to be a good fit for everyone out there because the main feature is actually support for manual saving of sessions (as windows mostly) and rename them according to your preference.
If an addon does not do what you would like it to do, I don't think it deserves right away a bad rating, it's just not something that works for you personally, maybe. All I can say is that although there are a lot of missing features that I might add in the future, the addon does what it was suppose to do.
The addon clearly was not made to compete with Session Buddy or other session masters out there, the addon main responsability is to store sessions as bookmarks and provide you with an easy to use interface to maintain a list of them.