What exactly MOD (Rectum) and MOD (Urethra) in the Clinic are intended for? As I understand once modded it can't be removed
The MOD can be removed by buying the corresponding Aid located far below the buying tab. As the description says, most of those MODs are intended to decrease the negative effects, like Injuries/Debuffs, on HP/STA. It's pretty good for mitigating the debuffs given by Abomination race's Sickly state, where for example Lona here went from 122 STA to 135 STA after being administrated all the necessary MODs:
You don't need Linked Glands, Taste (will make Lona vomit by eating any food), Breast A (only good on Hard difficulty) MODs. You can get Sterilization MOD if you want her to not get pregnant.
Though applying those MODs means Lona's arousal will increase even outside of sexual event. You don't exactly want her to orgasm during battle, so it's reccommended that you implement the MOD (G-Spot Removal) to prevent that. The con of this MOD however is once Lona's arousal point is in the red, she can't get out of it until she climaxes, and since this MOD prevents climaxing, her STA will slowly decrease so long as that arousal point is in the red, only slowly however so it's not much of a problem since the arousal point will be restored back to normal after half a day passes.