My thoughts and interpretations:
The penalty is with the number of planes that actually show up to fight, not the number that fly from the base.
Radar assists in making sure that the planes flying actually intercept the inbound raid as I understand it.
The hex is 30 miles across, thats a lot of airspace to patrol. To be in the right place at the right time is what radar provides you.
The planes you assign to CAP are flying in small groups over that whole area. Radar kicks in at making sure all the planes show up in the right area to intercept the raid.
No radar means that some of your guys are still flying at the other edge of the hex when the attack rolls in.
I do not believe UV reports a difference in the actual numbers displayed during the combat phase with the pictures, but you can certainly see the effectiveness difference represented by the end result. This is why sometimes you see a situation where planes show up and the air to air display shows the fight yet nothing actually happens. The CAP was there, but failed to intercept. The number show is the amount of CAP flying in the hex, not the amount of CAP that successfully intercepts the raid. That is show as individual aircraft shooting at each other.
Pretty tough to be sure, but thats what I feel we are seeing. Watching the actual combat plane by plane gives you far more information as to what actually occured. This information is not available in the rounded out AAR when it simply tells you that the 50 fighters where in the hex when the 50 bombers showed up.
There may be an additional benefit where high performace aircraft scramble to intercept the raid on top of the percentage you set. This may in turn be a function of whether or not these additional planes with tasked with other duties or not. In other words, if you set 20% cap, 80% escort, but no raids fly needing escort, it is possible that behind the scenes those 80% are shifted over to CAP that scramble IF a raid is spotted inbound. This effect may or may not be in play.
One of the confusing things that still leaves one guessing: Does altitude actually matter for CAP or does the altitude setting actually apply to the other portion of the aircraft (escort or sweep)? Always wondered myself...
So much gueswork with the manual vs the game, this is probably the very first wargame that ACTUALLY managed to hide you enough to force you to play at the theater level and really not be able to micromanage simply due to the lack of information available
Us wargamers are all the same, we want to get down to a level where we know the most trivial detail. I think if we actually had the access down to that level, UV would have been a total flop instead of a great game.