Users Choice ! Do you want to start whats needs to run manually or, do you want the system to do it for you.
Certain items hardly ever get used and should probably only be started manually.
Those items that you always use like Dropbox to back up certain files, are much more useful when started by the system.
If you start programs at system boot, you simply need to realize that it will take some extra seconds to boot your system.
If you want a quick system boot, then don't start programs (mostly utilities) at system start and waste your time starting them manually
after the computer boots.
Your computer your choice. IMHO, there isn't a right or wrong way of doing this. It's up to the user for how legitimate programs are started.