Why do I have to "transfer purchases" from my iPad when syncing to iTunes?
This process assumes that iCloud is not enabled.

It is possible to update apps on the device without doing so in iTunes. For this to work you will need to have enabled automatic downloads.

If you sync your iPad with iTunes without transfering purchases you coukld end up with older apps and losing the updates.

With iCloud there is no need for you to sync with iTunes, so if a device is plugged in iTunes would assume that you do not use iCloud and will transfer all the updated apps to the computer.

All in all it is more of a safety precaution if you are already using iCloud.