I think it matters because of the way the normals are interpolated across each triangle, from vertex to vertex. If you've ever painted vertex colors, you've seen how a quad's internal edge affects the gradient across it.
Ideally you'd just talk to your programmers and get them to make sure the model format you export takes the vertex normals directly from your app :) That way you know that whatever you see in your app is the same as what you see in-game. And it also means you don't have to worry about the triangulation because the vertex…
I'm confused why invisible tri edges would even matter? Surely baking normals only looks at vertex normals, which should be identical no matter how the edge is turned, or am I misunderstanding the process? Either way, I've had this problem and it was a big annoyance, so I'm glad to at least know a workaround.
The same thing happens in modo. The triangulation of quads in the viewport and in the renderer/baker is the opposite of how the quads get triangulated when you run the Triangulate tool. (You can test it by twisting a cube and then hitting triangulate.) Which means that if you bake your normal map using your quadded model,…