Ya, having created the app and the setup, just when you begin to feel that all the work is over, having to do these many things to get the installer to run does sound like too much work. But my opinion is that
VB's "Setup and deployment wizard" has long been relegated to the ranks of mediocre installer making tools. I gave up using this wizard long ago. If you want to create true professional looking setups that can be configured to take care of "all those issues", try something like an Install Shield.
Regards
Ankur Verma