The thing you have to watch while its under warranty is that chipped ecu's can be picked up by VW's test equipment and if you have a warranty claim they can void it because its been chipped.
There are companies that do a plugin box that you can unplug if it goes back to the dealer for anything and it don't reflash the ecu so no one knows its been fitted. I don't know if your Jetta is a 140PS thats what the link shows but you can search for any make or model?
If you were to hide the tune from the dealership, that would be warranty fraud. My dealer knows my car's modified. Their techs are terrified to touch parts of it because they don't really understand why it's still working with the way it's set up. The tune by itself doesn't really buy any significant jump in mileage, but it does make the car much more fun to drive. If you add the PDE down pipe and exhaust, with the tune then you can pick up about 10% on mileage. My dad's regularly getting over 600 miles per tank on his 2011 Golf TDI. On a recent road trip he got nearly 700 miles per tank."Just looking for a little extra hp & torque / fuel economy etc... what would you suggest?
box or flash"
I have been researching this topic for some time while I have been trying to figure out whether to go 'new' MK6 or buy old <MK6. I sent off an e-mail to Mark at Malone Tuning which is listed as "Alligator" on the basic performance mods page off the 1000q page. He stated that the chip tune may be noticeable by the dealer but more than likely if any repairs require driving the car they will certainly suspect and then look for mods based upon the clearly better performance. Then it is a matter of whether your particular dealership's service crew and management are gonna strip your warranty, more likely rather than less likely in my opinion. The other key factor that Mark mentioned which some people do not necessarily take into consideration is that changing the tuning may also require changing the tuning IF you have a DSG automatic transmission. The advantage of chip tuning over box tuning is that chip tuning is customized specific to your cars performance which is not necessarily the same as even the car before it off the factory line or the one after.
If I make any mods I will post them