I took out the Smart Cover when I bought my IS. It was an ex demonstrator and just over 3 months old but still in as new condition. I took the cover out as I did not want to worry about any small scratches or dents spoiling the good looks of the car and thus gave me piece of mind. I chose the Lexus Smart Cover as I thought they would be able to match the paint better and were approved by Lexus. If you take out your own Smart Cover it may be cheaper but will they be able to match the paint as well.
I also think it is worth considering if you are on a PCP deal where you expect to hand the car back after three years. If the car is in anything but perfect condition after three years you will get charged to put it back into perfect condition. As is what happened to me. I got charged for new windows as the CT had scratches on the privacy glass (However the Smart Cover does not include glass so would not have helped in this instance). With this insurance you can keep the car in perfect condition.
If you intend keeping the car longer such that at trade in time it will just get put to auction by the dealer, then the condition is not so important so the Smart Cover may not be of benefit. Especially if you are not too fussy about little knocks and scratches.
I also took out GAP insurance but found it to be half the price from my own insurance company as opposed to the Lexus one.