Can two independent office-js based PowerPoint addin and VBA based PowerPoint addin are packaged into one?
From Office-JS & VBA Addin How to mix together, I understand two office-js based addin and VBA based addin cannot communicate each other.
If these two addin does not need to communicate, VBA (maybe C#?) part and JS part can be bundled into one?
Of course two addins are distributed independently, but these are coupled with CustomXMLPart. Thus if this is possible, it is convenient for user.
Can two independent office-js based PowerPoint addin and VBA based PowerPoint addin are packaged into one?
No, it is possible from their nature. Office web add-ins are just web applications hosted somewhere on the server and run in the embedded web browser.
VBA macros are just scripts that are located on your disk/macro-enabled files. You are responsible for copying such files (deployment). Frankly speaking, VBA is not designed for the distribution process. That is what COM add-ins were introduced for.
If these two addin does not need to communicate, VBA (maybe C#?) part and JS part can be bundled into one?
Nope. They are entirely different. One is a web application and another is a desktop application.
All communication between different kind of add-ins can be built on modifying documents somehow. There is no any direct mechanism for that.