The power train warranty will be blocked/voided if it goes in for service of internal engine and or transmissions components. If for example the alternator or other engine accessory goes out they may not check the codes and replace the part under warranty. At any rate it's always a risk but then again if you start getting nickeled and dimed in repairs you could trade it and get a new or slightly used one with warranty. My guess is that a tuned truck driven within reason will be ok. The 5.3 gains nearly 30 hp and tq with E85 so I think the drivetrain could handle a tune without issue.
Chevy engineers are missing out on extra cash if they offered factory tuning which didn't affect warranty. They could offer stock, mild, and wild as choices.