Semen is not itself unhealthy if it contains no infectious pathogens. If it were naturally unhealthy then women would always be at risk with vaginal sex.
So long as you both remain 100% monogamous and have tested negative for HIV and all STDs for 6 months previously, unprotected anal sex can be considered safe. You get HIV from a previously infected person; it does not occur spontaneously during anal sex with a negative partner.
Regarding your follow-on question, the primary role of the rectum is not to absorb as the large intestine does. The rectum's job is to temporarily hold the stool until it is evacuated. Semen deposited in the rectum may therefore remain there and not be fully absorbed, being expelled with the next bowel movement. Or in your BF's case, since he probably didn't have an intervening BM from when you had sex, the semen remnants were released when he passed gas. This would be normal and no cause for concern.