IOS – be signed into iTunes with a different account than iCloud on same iPhone at same time

In any of the common scenarios in which you store your Store credentials on devices under the control of others, it makes good security sense to have those be different from the ones you use for iCloud.

For example, it is common to share music among family members by using an Apple ID for purchases on all of the family's machines. If that Apple ID were the same as the one you used for iCloud, then (unless you can be sure that all family members have secured their machines) anyone who got his hands on one of those machines could potentially gain access to your e-mail, calendar, and documents (and, in typical configurations, could even log on to your machine if he had access to it).

The iBooks app on iOS as well as OS X Mavericks uses the account you use to sign into the iBooks Store for syncing bookmarks, notes, collections, highlights and purchased books. So if you share an Apple ID/iTunes Store Account for purchases from the iBooks Store, then the sync will affect all the users who share the account.

The iBooks sync is not based on one's individual iCloud account, which is used for iMessage, FaceTime, Mail, Calendar, etc.

See iBooks: How to sync iBooks between devices for more information.