I do not believe there is any one right answer to your question. It all depends on your business requirements. I have worked with applications where all of the web interface was done on the System i, where all of the web interface was done on non-i server and the application utilized System i application databases in real time, and where all of the web interface was done on the non-i server with periodic file transfers between the non-i system and the i.
All three approaches are viable and provide different advantages and disadvantages.
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