Quantum superposition of high-dimensional states enables both computational speed-up and security in cryptographic protocols. However, the exponential complexity of tomographic processes makes certification of these properties a challenging task. In this work, we experimentally certify coherence witnesses tailored for quantum systems of increasing dimension using pairwise overlap measurements enabled by a six-mode universal photonic processor fabricated with a femtosecond laser writing technology. In particular, we show the effectiveness of the proposed coherence and dimension witnesses for qudits of dimensions up to 5. We also demonstrate advantage in a quantum interrogation task and show it is fueled by quantum contextuality. Our experimental results testify to the efficiency of this approach for the certification of quantum properties in programmable integrated photonic platforms.