I took that comprehensive perk or whatever it is called. It said it gives you an extra point whenever you read a skill book. But its giving me 4... Yes no?

With the perk you get 4, without the perk you get 3.

they give you 3 without the perk. 4 with it

Oh i thought it was 1; the same as Fallout 3. Aww why did I take this perk...

That perk is still one of the best in the game IMO, though not for the skill book bonus. What its great for is the skill magazine bonus which makes all the magazines (which vendors restock) give a temporary +20 bonus letting you keep skills like science speech and lockpick lower than you would otherwise need them to be for the occasional difficult skill check.

wait are you serious?

As a heart attack.

With this, if you have a magazine, you never need to have your 'auxiliary' skills above 80.

Get retention as well, and the effects last 3x as long!

(you DID read the perk description right? It -TELLS- you this)

He's right....I have comprehension and get +4 points from books and +20 from magazines. I'm currently working on getting Speech and Barter to 80 so I can win any challenge. Using two magazines got the Boomers eating out of my hand.

A Note on magazine bonus UI issue.
Any item that gives you a temporary bonus like some food have an indicator of benefit and how long it will last +1HP(7s).
Magazines only indicate the benefit but not the time limit after which they expire. I found this confusing after 'reading' a few magazines...