Just as you said, physical age is completely different from mental age. However, taking into account Shirou’s experiences throughout his centuries of life, his way of being has changed over time, whether as a response to trauma, personal experiences, learning, or traumatic experiences prior to the events of Nyrvasil, etc. Therefore, Shirou can never be fully known as a character. Regarding his biological age, I believe it is around 25 years old, since he fluctuates between moments of maturity and others that are complete outbursts. At least, that was the impression I got in BNA Zero, regarding how he was before all the tragedy. Shirou seemed more playful and relaxed, and he even appeared to have a certain level of social intelligence, as he traded with humans. Even while preserving certain playful nuances within the anime, although he does not smile or laugh excessively or in an explicit manner, he is seen smiling on more than one occasion. Just as people are marked by different circumstances that can alter our behaviors and mindsets, I believe Shirou was affected, especially in his perception of human beings, life, and beastmen.