No, from what I understand this only affects binaries through Gatekeeper. Gatekeeper is “opt-in”—sort of. The way it works is that your web browser has an option “LSFileQuarantineEnabled” set in the bundle, and this makes it so files it creates have the “com.apple.quarantine” extended attribute on them by default. This attribute is propagated when you extract archives. When you open a program with the quarantine bit, you get the Gatekeeper warning.

All MacPorts has to do is either avoid setting the quarantine bit in the first place (easy enough) or remove it. The quarantine bit is nothing more than an xattr called “com.apple.quarantine” which you can inspect or remove with the xattr tool.