so this behavior is "normal" for the ZD2 isn't it ?
i think you forgot soemthing important :
With the older release (ZD1), as i could install the whole app (soft+data) in one drive, i had 2 big advantages which disapear now :
1 - the ZD could be portable : i could install it on a USB key and bring it on any windows pc where ZD1 was installed in same location (always on E drive never on C) !
2 - i could install it on a net drive to perform a backup of my own mailbox (more than 2GB of data is very long to synchronyze) for offline browsing. Then when i was installed it (Holly ZD1) on a net drive, i was sure the mailbox was very protected (don't forget all the emails (aka the .MSG files) are fully clear and not encrypted !!!) As we know, a windows desktop user account is very unsecured, so storing the mailbox there is like putting a money bag in your flower box !
Moreover, now, as my store folder (mailbox) of 2 Go is installed in my default account windows folder, that means zimbra desktop cannot be "user-friendly' used in a windows environement network with roaming profil (win server 2003,2008..) cause the profil is uploaded on local machine at each login session. Do you imagine a 2Go profil download trasnfert at each openned session ? Even, do you imagine the re-upload time profil when the user will close his remote session ? The administrator will not install any mail on a local unsecured drive, and by the way the standard policy of capacity for system drive is ofter short so, like me, the users will be out of space !
Don't you want Zimbra desktop to be use in a wide firm under a windows network without Exchange ?

Then you had to consider this roaming profile utilisation.
The best way for this wizard should have be to let the user choose the install path directory AND the default location to store the main data.
Well, as it is a beta release, maybe you shall consider my notices....
PS : by the way, Outlook (and surely Thunderbird) let you choose the folder for storing your PST mailbox)
PS2 : and i didn't speak about Mandatory profiles with this ZD2 : at each log session, user will have to resynch his mailbox cause :
"A mandatory user profile is a preconfigured, read-only roaming user profile that administrators can use to specify settings for users. With a mandatory user profile, a user can modify the desktop, but any changes made are not saved when the user logs off. The next time the user logs on, the mandatory user profile set by the administrator is downloaded. There is also a special type of mandatory profile known as a super-mandatory profile."
source:
Roaming user profile - Wikipedia, the free encyclopedia
PS 3 : and i never stored any personal data on the system drive cause in 95% of any situation, it is this hard drive (or partition) which will crash in first place or attacked by virus.