We held meetings and weighed the pros/cons of each option and using component based had far to many problems. We decided to use file based because of how we design reference projects. There are major issues with copying designs and projects. When Bentley resolves the issues with component based, it will be very easy to move in that direction. Yes, you can run isometrics with a file based environment, the creation of an i-model is required as a middle step. This functionality is greatly enhanced in SS5.
I understand what you're doing with the pipelines. It's too bad that you can't have transparent insulation.