So, why would a perfect game need a "patch"? Because even the gold standard has minor flaws, and the ROM scene is all about perfectionism.
The safest way to verify a patched ROM is by its checksum. A clean ROM has a specific SHA-1. A "patched up" version for AP will have a different hash. Use a tool like ROMnalyzer or consult rom-hacking forums for the specific hash of the latest v1.1 AP patch. Chrono Trigger Ds Rom Patched Up