On the warranty point I’d say it depends on where you bought it, it’s the dealer you deal with. If he doesn’t care then everything will be fine. I can’t imagine there being an issue at all with a battery or the motor they have nothing to do with wheel size. Could potentially be an issue with the frame front end but I’ll I’d argue not if you’ve kept the head angles within acceptable limits and you do this by not going crazy on the front fork height. Of course, if you keep the stock wheels and fork, you can always make them stock when it goes back to the dealer.
If you're buying to convert then the Comp makes more sense, unless you specifically need or want the bigger battery or mastermind TCU.
Handling wise, on tight single track there isn't much difference on my setup, but the bike feels faster everywhere. I have gone conservative on the fork, which is the Rhythm at 170mm, so the bike's front end hasn't been raised much and the wheelbase and head angle are close to stock. Also, I chose the smaller of the two frame sizes that would fit me to keep it more agile/playful. So consider the frame size and what fork you are going to use if you're buying to convert to 29. If you buy a larger size and fit a Fox 38 and 29wheels this will inevitably impact its abilities in the twisty stuff. Check out Rob's video, he covers pretty much everything.