It's fine to add after run oil to the air intake on the carb. While it's kinda poorly stated in the manual, what they mean is that you shouldn't add the after-run oil thru the carb's fuel fitting. That can cause the needle valve o-ring (if equipped) to swell, causing trouble in the future.

Adding thru the wide open throttle barrel is the best way. Personally, I turn the engine so the rotary valve is closed (look down the carb throat and turn the prop, you'll see!). Then I almost fill the carb with after run oil, and then turn the prop over a few times to get the oil into the engine. It gets sucked in just like the air does normally. This method gives you a decent sized "measuring cup" that varies with engine size, pretty much assuring that a decent amount is added.

J