Does the iOS Keynote laser pointer work when using the remote?

I believe the answer to your question is no.

I use Keynote's Integrated Remote function on my iPhone 4S to control my Keynote presentation on my iPad Air. It works well over wi-fi and bluetooth (a touch of delay on bluetooth). However, I am not able to get the virtual laser pointer to work by touching the screen on the iPhone.

I have not yet tried using the iPhone as a remote while the iPad is hooked up to a projector.

Yes it works for me in the new 6.2 version of Keynote. Presentation on the iPad Remote on the iPhone. Remote works and the laser pointer and drawing tolls work just fine.

Look here to set up your remote properly....

http://support.apple.com/kb/HT6112

Correction .....It's version 2.2 on iOS and 6.2 on OSX....Sorry about that.