It's tailor made versus off the rack. With source (ports), you can choose non-default options and settings to fit exactly, but it takes longer. Packages are quick and one-size-fits-most.
Seriously though, the deal breaker for me is that the package system has no built-in checking of security hashes (e.g. unlike Ubuntu repositories for example). For that reason, I put up with the compile times.
The vast majority of the time I leave the compile options as default.
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