The purpose of the Product Preferences widget is to tailor your eSupport experience. This means that, after registering an interest in a product, users will see Alerts and Banners which the authors have categorized as related to that product.
With over 115 active products, we roll up the Product definition in this widget to "Product Family" level, to keep things as simple as possible.
As you point out, the former Integrity and Atego products were recently brought into the Windchill family. Windchill is available for selection after choosing "Product Lifecycle Management" on the first screen.
Please use this for now (and yes, it will mean that you'll see some Windchill Alerts and Banners for a time).
In the meantime, we've initiated a change request to add "Windchill Systems and Software Engineering" to the list of product families, and will reply back to this thread to let you know when it's available.
Thanks again for taking the time to report this. We appreciate the feedback, which helps us to improve the experience for all.