Hi Mark,
The checkbox for really delete users was just implemented as a way to make it possible for the IT guy to bail the site admin out if he accidentally deletes a user. The IT guy can find the user in the mp_Users table and set the IsDeleted field to 0 to un-delete the user.
So you could find a list of deleted users with
SELECT UserID, Email from mp_Users WHERE SiteID = 1 and IsDeleted = 1
Then upon finding the UserID of the one you wanted to un-delete you could do
UPDATE mp_Users
SET IsDeleted = 0
WHERE UserID = thUserIDYouFoundBySearching
It was never intended as a way to casually delete and un-delete users from the UI and I don't really want to add such a feature. If your client is deleting them accidently frequently I would caution/train them to try to avoid doing that, it should be a very uncommon event. The main goal was so as not to lose data in cases where the user may have a purchase history etc.
Regarding the localization question, sorry that document is badly out of date. Back in the old days we used a timeoffset but currently we use a timezone id and we are able to adjust times correctly even during daylight savings time which varies by time zone and time of year (except under Linux/Mono where we still use the old offset way since we could not get the new way working).
User time zones are set on the user profile. When new users are created they get the site default time zone, unless they chose their own, but changing the site default timezone does not affect existing users.
You no longer have to worry about config settings for time zone localization it is done from site settings for the site default and from the user profile/user management page for users.
Hope it helps,
Joe