When you start Pd through Rosetta (by right-clicking the app-icon and selectign "Open using Rosetta"), you instruct the OS to launch the Pd-GUI through rosetta. The Pd-GUI then starts the Pd-core, and doesn't care a bit about your rosetta-settings, which means that the Pd-core is started in native (arm64) mode.
Are you sure? I thought that when a universal binary is executed as a child process, it will "inherit" the architecture of the parent process by default.
Christof