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Uh… no? Unless you really customize all the options I guess. There's no reason to rebuild the exact same package you'll get from the repo.

E.g. I install all firefox's dependencies from pkg, then I build firefox from ports with the GTK3 option. Same with packages that use openssl (I use libressl). Never had any problems with that.

You can mix and match. The only problem comes if you have flags in a dependency that don't match the flags in the package pkg wants to install. A bit bothersome, but it allows you the best of both worlds.

As floatboth said, there's really no reason to build every minor package by hand. Only those that you want to change the config or their dependencies.