I think you are confused relative to the meaning of the out of the illegal sub superseding the penalty for BOO.
In your situation 1, the offense isn't "charged" an out.
The illegal sub (Lee) is declared out. That means his out is attributed to the position into which he illegally "subbed" (which is Smith's spot). This out supersedes BOO---which means you will not also declare Smith out for the BOO infraction. One out only is called for the infraction of illegal sub Lee entering the game. The next proper batter would be White---who follows the batter who should have batted (Smith). Smith is considered as having been removed from the game when Lee entered, and Smith may reenter the game if he still has his reentry privilege.
The declared out on Lee as an illegal sub must be attributed to a batting position and an at bat, and that position was the one originally occupied by Smith.
With that understanding, all your others questions should be answered.
Just my opinion,
Freix
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