This has nothing to do with iCloud. You have never been able to sync the same media using two separate iTunes Libraries. So, if you are wanting to, say, sync your Music between two libraries, iTunes is just going to overwrite whatever the other iTunes library put on your device.
If you are talking about syncing different media, then that can be done. So, you could sync your music with one library and your photos with the other one. But if you do that sort of thing, you have to make sure that your Device Profile screens for each of the media types is set up correctly to do that. In the example I am providing, the Sync Music would be on in the device settings on one computer, but on that same computer, the Sync Photos would be turned off. In the Device Profile screens for that device in iTunes on the other computer, Sync Music would be turned off, and Sync Photos would be turned on.
That is how separate syncing between iTunes libraries on two computers has always worked....
Cheers,
GB