if you are unsure about auto-remove just look up the man pages in the terminal.
i only use the software center to find info or discover new software related to certain criteria but i always install from the command line. when there are .deb files provided from the vendor then i also install through CLI/terminal.
i only have one VLC instance not two.
i’ve found that auto-remove works equally well globally as it does applied only to specific programs. for me it makes little difference.
my only complaint so far is that the default gnome 3 app drawer isn’t better organised. some applications bundle more than one GUI utility and end up making a mess everywhere.