Why does instant coffee have less caffeine?
Caffeine is water soluble, but it takes a bit of time to be absorbed by water. 

What determines the caffeine content of a coffee process is how much time it spends with/in water. 

For example, a bodum French press will pick up more caffeine from the coffee since the grounds stay soaked for a while.  Drip coffee will have more than a single espresso (common misconception is to think the opposite). 

It's likely that the instant coffee process passes the water through the coffee under pressure and faster than drip.  This will naturally prevent the caffeine to be absorbed in water as much. 

Besides using decaf roast, what you may wish to do is get an americano coffee made with one or two Ristretto shots of espresso.  A Ristretto shot is usually pull away after 10 seconds. 

Take a look at this analysis from the Mayo Clinic for the actual Caffeine values.