When you restore your data partition with recovery, you are restoring the backed up userdata.img file, with literally everything you have done since the moment your phone booted the first time after flashing a clean rom. This includes everything you've done since the first time you restored a data partition with this method, assuming you've done this repeatedly after flashing several times. Any issues you had with permissions, etc. located in the /data directory will be carried over. Also, depending on what rom you are coming from/going to, you may encounter incompatibilities between some things that this will restore. For example, if you backed up a ported sense rom and restore it after flashing official aosp, you're most likely going to get a bootloop because some things are non-existent in one rom or another, or may require different permissions.
When you restore app data only (we're not talking about call log, texts, wifi apns, etc. from the system files....those are fine to restore with TiBu) all you are restoring is the saved data for a given app. This is not like restoring your android user data, because it won't restore android settings, and other changes made to the android system from within the /data directory. It will get you probably 90% restored to how your device was before flashing, and the rest (like the system settings, etc.) is up to you to do manually. This is the best way to ensure you will have a nice solid running rom, and guarantees no issues that may have existed in your last rom won't be carried over. Even when you are just flashing a new update, you never know what incompatibilities may exist between releases when you restore the whole userdata partition.
I'll give you an example of what I mean. Let's say you are playing around in an official aosp rom with developer options and it results in a bootloop. If you back up your rom with recovery, wipe all partitions, reflash a new rom, then restore the rom data, you will get a bootloop for the exact same reason you did prior to wiping. If, instead, you have a current TiBu backup on hand, then you can full wipe with recovery, flash a new rom, then restore with TiBu. Your bootloop will be solved because it won't have restored your incorrect setting that resulted in the bootloop in the first place.