From my limited experience there is very little difference between what the 2 do. However, the obvious difference is that with the bundled power supply, you do not have to install it into the case.
Generally the bundled power supply is a generic standard power supply. If you wish to modify your system you can go to power supplies that have greater cooling capacities, different power protection etc.
Depending on the system you are building, this will determine what you will want in a power supply. No doubt somebody else more experienced than I could assist you if you were looking for the 'best' power supply.
I hope this limited information is helpful.
Cheers!