All these plug-ins only change the pedal position the computer sees, for instance, you put your foot down 10%, the truck will think you put it down 15 or 20%. If you're looking for gains that make more power or want the tune dialed in for your specific truck, you'll need a tune. It will throw a code on the PCM but some tuners can get around that. Also, you'll need to get your PCM unlocked before you can tune it. As far as tuners go, it depends who is writing the tune. Some use Diablo, some use HP Tuners, some can use both. I'd look for the person before the tool.
To answer the question about the pedal commander, banks, and the Diablo Pulsar...all can be removed without a trace before going to the dealer.
Along those same lines, if you have a tazer DT or anything else to bypass the security gateway, make sure that is removed before going to the dealer for anything. Some dealer will flag your truck if they find one of those and then your warranty will be out the window.