Why: user's data is user's personal property. As the "personal" indicates, it includes user's own data. What rights has the package manager to remove that data? This may happen while a user is logged on. How happy would you be to see files disappear suddenly under you?
How: a package is installed system-wide. A user data is per user. The package is removed by root, or one specific user if capabilities are used. What to do with other users data? Should the package manager start scanning all user's home directories and cleanup files under them? Is it wise to let the administrator or a simple user decide when it is appropriate to delete others users' files?
All considered, a cleaner application sounds not so bad. At least each user decides for himself if and when to delete things.
A note about the source of my bias: I have been hit a few times on Windows by applications, like drawing or document tools, that by default store the user's file into their own folder, something like c:\Program Files\XYZeditor\Documents. When you remove the software, the folder is gone, and so is your labor of love. Sad. Professionally, I work on train control systems that create historical records. We take _great_ pain of organizing our software so that we _do not_ remove any user data if our software is removed or upgraded. This data is important to the users, since it records their past operation events, which events have occurred (and these records may have legal significance) no matter if our software is removed or not.
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