The ecosystem will change, no doubt about that. Just like it changes when we start agriculture somewhere, or pastoralism. Even if we consider that the new ecosystem of desert with a lot of shade might affect neighboring pristine desert within quite a radius, there will still be a lot left in the foreseeable future. Very much unlike agriculture and pastoralism, which have been pushed into almost every corner even remotely viable for millennia.
It might be worthwhile to exclude certain areas of particularly rare variations of the ecosystem to be built in. But it's easy to end up with too much red tape that will be abused for NIMBY and by people who hide a fossil yolo attitude behind a facade of conservationism.
Perhaps there could be some mechanism for operating some veto quota, "pick the project you want most desperately to be stopped"? That scheme would probably end getting gamed in the ugliest ways, with sacrificial decoy projects getting proposed, not vetoed and then getting built to keep up appearances. Better not, heh.