The reason stock tunes don't damage the car is the same reason you can get such gains on a fully-custom tune... they leave a ton of leeway in order to prevent engine damage.
Even on high economy cars like, say, the Mirage, we're seeing parts of the engine map on the dyno that default to a very, very rich running state during certain drive situations... such as low rpm under load, or at cruising rpm.
A canned tune can fine tune these maps and remove some of the waste, but tuning specifically for maximum economy on a canned tune is like tuning specifically for maximum power. It can cause problems when you get a batch of bad gas. Or if one of your customers lives in a very hot environment, or at high altitude, or etcetera.
Custom is where it's at.
I'm not surprised Vekke can get 10%... though that is a delightfully high number on a car that's so efficient from the factory. On one propane conversion, we saw a change of around 30% when the ECU was retuned.
...because that particular motor defaulted to an AFR of 10:1 at idle.