It was a well-known fact that being a State Alchemist had certain perks. They were given “research” money and weren’t required to wear uniforms and show up for the nine to five grind. They were eccentric and allowed to do almost anything they pleased. Spoiled some soldiers said; yet, the military turned a blind eye because a happy alchemist is a productive alchemist and happy productive alchemists generally refrained from overthrowing the government.
If peculiar noises came from the officers’ restroom after Colonel Mustang and his Second Lieutenant walked in, nobody asked, nobody told, and nobody saw a thing.