MacPorts and Homebrew behave identically here: precompiled binaries are not affected, only .app (and similar) bundles.

(People find this confusing, because Homebrew does a superset of what MacPorts does: it distributes both source/binary packages and it distributes "casks", which are essentially a CLI-friendly version of the App Store and come with macOS's additional restrictions on applications. This only affects casks.)

The hierarchy is actually a little more complicated than this. MacPorts can and does build open source GUI apps (in fact it largely rejects binaries for them, preferring to build them directly). Homebrew rejects GUI apps from being built from source. Because Homebrew downloads apps from the internet, it makes them with the quarantine attribute, which means more apps that it handles will be flagged by Gatekeeper.