If you want to modify your car, there will be something on it that can be defected. The only thing that you can do is do it smart. Avoid any obvious stuff.
Don't have your car too low, invest in adjustable height coilovers and make sure you're at or above the 100mm.
Don't have an atmospheric BOV.
Just use a stock airbox, the pod doesn't gain anything, and if you really want the pod, box it up properly.
Don't get too crazy with your wheels.
Think about not having a turbo timer, if you've been driving normally and off boost you don't really need it, and if you have been driving hard, just let it run for a minute before you turn it off.
Keep your exhaust quiet, big arse mufflers to take the edge off it, drone and db levels.
Keep your turbo low mount, a hypergear highflow is pretty good for this.
You can make good power and keep your engine bay looking pretty stock, you just have to think it through before your build.