Although UI developers can find a way to hide the OOB panels in the source HTML files however as there is no concept of safeguarding these customization in the product right now, any such any changes that we are making to the HTML files will be overwritten on UI upgrade.
Also lets take an example, if I create an option which allows the end user to choose the Operating System / Installable resource as options and name this category as "Operating System", in the CLM Web Portal App the end user will see this option under "Operating System" category. In addition to this, the default panel of Operating System which shows the Installable resource selected at the Blueprint level (which will get replaced by the Option) will also be shown. This adds to confusion.
Perhaps there should be an option to show or hide certain panels just like Console Preferences tab in Midtier which allows the User to extend this functionality of hiding / showing OOB panels in CLM Web Portal App or rearranging their sequence order.