May be the freebsd build is using some binary library packages?
A cursory search indicates that one of the freebsd 'build-scripts' used for installing obsidian uses a binary package for obsidian itself, not building it from source.
It strange that about obsidian which seems to be rather popular here has many people thinking that it is open source, when it is not.
That's just a user contributed thing though. It's also just in the official ports collection. There's only a makefile there and some config files for electron (electron is kinda a PITA to compile on FreeBSD because there's no package)
Now, it can update itself automatically but it's all JavaScript. No binaries.
But it's safe enough for me anyway. Especially because the dev community uses it do much. If it did something untoward it would be noticed quickly.