Earlier quoted context omitted.
I'm assuming you don't use the package manager like Homebrew or MacPorts? this is where the gatekeeper will annoy the hell out of me. Apps installed via Homebrew often will encounter Gatekeeper alerts. Half of them will give the option to open it and the other half, the gatekeeper --demands-- gently ask me to put it in the Trash without the option to open it.
Macports doesn't give you any headaches, it follows Unix principles. Homebrew is a keg of worms, if you excuse the bad pun. Sadly (because it seems to be easier to get started?) many developers prefer it over Macports...
It is likely that it is not the devs prefers it over MacPorts, it is likely that end-users prefers it and the devs are following what the end-users desires. Homebrew have huge catalog of software and libraries than MacPorts.