Of course cutting a big hole in the down tube will effect stiffness. Less material, less stiff. If they’ve done FEA finite element analysis I’m sure they have a good understanding of the stiffness losses involved.
( it would also depend what size frame they tested )
One things for sure. A big hole isn’t going to make it more stiff unless that add a lot more material, which will equal more weight.
It’s like having a car and making a convertible model. The convertible will be less stiff unless they add more strengthening/ weight.
ÌMHO it’s absolutely nothing to worry about. And it absolutely won’t affect real world handling. Geometry, and centre of mass will have a far greater influence on that.