There's really no way to pressurize bottles before capping, as you'll just release that pressure going from your filler to the capper anyway.
That said, you don't necessarily need to pressurize before putting liquid in, either. If your filler has a stopper, then as liquid enters the bottle, the air it displaces and compresses functions as the counter-pressure. (I've never used a beer gun, does it have a stopper?) Your filler will stop once the air in the bottle is compressed to the same pressure that's on your keg, so a slow release of pressure will slowly fill the bottle and thus reduce foaming by keeping a slightly higher than ambient pressure on the liquid as well as decreasing turbulence in the bottle.
The only reasons to pressurize before filling would be 1) to start the flow of liquid slowly to minimize turbulence and foaming as much as possible, and 2) if you're bottling beer, flushing with CO2 will reduce contact with oxygen and minimize skunking so that's not a concern for soda, unless you have hops or something else in there that could go skunky.