Hi EwanG,
Based on my understanding, if your app or game only need to read or save file with user-demand (instead of programmtically access the files in some well-known folders without user awareness), then you can just use the file pickers without declaring the certain
folder permissions (such as Music Library, Picture Library or Document Library capabilities).
#Quickstart: Accessing files with file pickers(Windows Store apps using JavaScript and HTML) (Windows)
http://msdn.microsoft.com/en-us/library/windows/apps/hh465199.aspx
#How to save files through file pickers (Windows)
http://msdn.microsoft.com/en-us/library/windows/apps/jj150595.aspx
Those capabilities are mainly used for those app which will directy access/manipulate files in the certain folders without informing the users (user might not be awared or interacted during the file accessing).
#App capability declarations (Windows Store apps) (Windows)
http://msdn.microsoft.com/en-us/library/windows/apps/hh464936.aspx
Here is a blog article which also mentions some suggestion on dealing with security and permissions when building windows store apps:
#Security best practices for building Windows Store apps
http://blogs.msdn.com/b/windowsappdev/archive/2012/12/18/security-best-practices-for-building-windows-store-apps.aspx
Please remember to mark the replies as answers if they help and unmark them if they provide no help.