For reasons having to do with our particular operation, it is our custom to build many packages from source code no matter the operating system, so I don't want to install from the ports tree.

The ports tree is just there for installation from source and putting the software after compile into canonical locations (and adding usually the necessary startup scripts etc. in the process - Ports are not to be mixed with packages.

As FreeBSD supports the source centric way from centralised location, there shouldn't really be any need for doing the compile outside the ports tree. You can basically tweak the ports to your hearts content (most of the relevant options can be tweaked from the ports Makefile already) and in addition the port installs into location using a method the rest of FreeBSD users can give you meaningful advice.

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