Handbuilt wheels are always going to be alot better than something put together by a machine. A full wheelset that is handbuilt is going to be just as good as buying seperate hubs and rims and having those handbuilt, the issue is just that you get something that someone actually took the time to put together properly.
As for building your own wheelsets, a really experienced wheel builder can do it by hand, but you'll need a tensionmeter. With a tensionmeter there's no reason you couldn't build your own set though