I will try.
At one time, everything opened from the same Multiple Document Interface could share information with other spreadsheets in that same frame. Hence you could cut and paste cells or specific formats or values from cell to cell. They all shared the same frame and settings. If you opened another instance of Excel (i.e., in another MDI Frame), it would not know about the prior ones you opened in the first frame and if you were to cut and paste from a cell in that instance to one in another instance, you would be offered the option of pasting it as text without any formatting or other cell characteristics. This confused users and Microsoft fixed it by defaulting Excel to share a single instance by default.
Now every time you open Excel by default it is all part of the same Excel Instance. No more questions about why it allows me to paste all settings from one spreadsheet but not another.
However, those of us who need to keep each Excel Instance separate (for example, if you are running a macro in one spreadsheet and want to report status in the status line, you probably don't want it overwriting the status of another macro running in another spreadsheet), still want to run multiple instances of Excel. A fairly good description of the opening techniques available is here:
Each instance is independent and does not (or should not) interfere with another. For example, I typically run scripts in 10 or more spreadsheets that monitor information from various sources. If one of these scripts encounters a problem, it reports it in the status line. If they were all part of the same Excel instance, every workbook would show the same status line error, making it useless to identify which script is encountering the problem. Also, the scripts do have some global variables which would likely cause problems if two similar workbooks were running similar scripts in the same instance.
Hence, even though it uses significantly more memory, I open each Excel workbook that is performing these tasks in a separate Excel instance, as I explained, to isolate them from one another. Groupy likewise refers to "instances" in its documentation, but based on your reply, it appears they consider each workbook as a separate instance even though Microsoft may consider them sometimes part of the same instance (if opened normally) or part of a separate instance (if opened using the technique described in the referenced page and elsewhere).
So given all of that, I think I know my answer, but it would save a lot of time and be far less error-prone if Groupy could recognize and open multiple instances of Excel and Word (probably not particularly useful for the other MS Office products) so that I could use Groupy to save 10 instances of Excel as a group and then open the 10 instances via Groupy rather than opening each individually using the Alt+Click method.
Task manager shows the workbooks opened by Groupy as all being part of the same instance of Excel. If you have true multiple instances, there will be an equal number of Excel entries in Task Manager.
I hope this explains this to some extent.