Thank you for the attention you've given to our JomSocial plugins just as we released them! Your feedback helps us improving their features.
We've just laid out the new version for Profile Designer (1.1) which will help to address certain issues when e.g. a user can't find the plugin if the Profile context menu is hidden:
now you can set in the BE plugin options whether you want to make it a core application or not, whether you want to show it in menu or not, and whether you want to show it in application or not.
Hope that will help to solve part of the questions and we'll work further on it.