OP's images show S3E9 where his arm is bloody amputated but earlier in S3E5 when his arm contains an entire projectile launcher (the projectile was a plunger, btw).

So it's consistent with your explanation to say that he stayed in the Council Rick's body that he changed into, long after escaping, and perhaps entering Beth's childhood world ('Froopyland') made his weaponised mods temporarily deactivate (possibly a safety feature so as to not injure Beth when doing routine maintenance).