I cannot modify the models automatically without having the artists to take a look. And doing it for a massive amount of
data is out of our bought).
That's what a build pipeline is for - you modify the models when they are imported without changing the source assets. That's not really any different to calculating different uvs in the shader when those UVs are calculated in a way that do not change based on other factors in the game.
You mentioned Unity, so I'll point out that if you are doing mobile games then multiple texture samples gets expensive very quickly based on the target devices. Older Android devices can be especially bad for this. Older mobile devices also struggle if you calculate the texture coordinates in the pixel shader. Blending is also a major bottleneck on mobile. If you are doing PC though, these points don't apply as the hardware is very different.
Its pretty important that you take the time to construct performance tests, even if you hand write them yourself.