All what I can say is that this is working as designed. I am also Qlik partner and similarly to you I often have to migrate clients from NP16 to NP17+ and i face the same issues. Migration is the process where we as Qlik partners have to estimate amount of work required to be able to migrate properly and often rebuilt and adjust existing QlikView application to work with new approach which in 99% cases is required.
What you have described is the most common and known issue and should be considered before migration - right? Documentation is clearly stating that email is unique id and you can't have 2 the same emails, but you can slightly twist it and create 2 dummy emails with the same alternative email which you would use in distribution. That will solve your first problem where you require multiple users having the same email (in NPrinting April 2020 you do it by creating multiple users with unique emails and the same alternative email and you use alternative email during distribution)
As per sending report not as zip file. As long as you don't introduce cycle report functionality you will get reports sent without being zipped. Unfortunately enabling cycle automatically zips ale reports into one file. This is again known, works as designed and should be considered and communicated to client before migration - right? All this information is available on https://help.qlik.com
The last thing "The processes and rule are so complex with multiple filters, conditions and API connections so its not possible to generate different filters or condition for each case" - I disagree with this statement. I understand it can be very complicated but it is still possible. All what it requires is planning and proper design. It is not easy, may require change and time to design, but it is definitely possible.
Sorry I don't have a better news for you - but it is what it is and as I mentioned above it migration needs proper overview and investigation of methodology used as it is not 1:1 with what you have in NP 16.
cheers Lech, When applicable please mark the correct/appropriate replies as "solution" (you can mark up to 3 "solutions". Please LIKE threads if the provided solution is helpful to the problem.