I suspect what could've happened here is that when the template was being created, you might've set it to you Products CPT instead of selecting "Don't assign to any posts". This could've been why this occurred.
I know the plugin isn't perfect and has many faults and issues. I do assure you that with each updates comes with improvements and new features.
Perhaps it may not be as easy as you would expect it to be now, and I certainly agree with you. However it has come a far way in terms of user friendliness and usability.
I'm sure this will only continue to get better as our development team continues to work on improvements.
What you can do is open a feature request ticket to help steer our development team in the right direction with a few features that you would like to see.
We take customer feedback very seriously as we aim to improve our products with your help.