This research is focused on modeling individual protein binding sites. Pleiotropic effects and off-target side effects are caused by interactions beyond the individual binding sites. So I don't think this tool by itself will be able to design a protein that acts in the way you describe (and that's putting aside the delivery concerns - how do you get the protein to the right compartment inside the cell?).
But novel binding domain design could be combined with other tools to achieve this effect. You could imagine engineering a lipid nanoparticle coated in antibodies specific to cell types that express particular surface proteins. So you might use this tool to design both the antibody binding domain on the vector and also the protein encoded by the payload mRNA. Not all cell types can be reached and addressed this way, but many can.
But novel binding domain design could be combined with other tools to achieve this effect. You could imagine engineering a lipid nanoparticle coated in antibodies specific to cell types that express particular surface proteins. So you might use this tool to design both the antibody binding domain on the vector and also the protein encoded by the payload mRNA. Not all cell types can be reached and addressed this way, but many can.