Well to define "all differences" would be near impossible because every
OS package is built differently. However, with that said...
1) Package installs are pre-built with their own options configured
which also gets installed wherever they decided to put that installation
once it's installed.
2) With the source, you are able to define what is built, where it
should be installed, etc...
So if you are going to install via a package, you are basically forced
into whatever options they set. Unless of course you decide to take their
package and then re-package it to fit your requirements. But that would
pretty much be a pointless as you'd be better off just installing from
source at that point.
Most if not all packages also comes not only with a simple install but a
simple way to uninstall the software. Where-as if you compiled and
installed via source then you'll need to manually remove the installation
if you no longer need it on your machine.