When forming sophisticated semiconductor devices including transistors with sophisticated high-k metal gate electrode structures and a strain-inducing semiconductor alloy, transistor uniformity and performance may be enhanced by providing superior growth conditions during the selective epitaxial growth process. To this end, a semiconductor material may be preserved at the isolation regions in order to avoid the formation of pronounced shoulders. Furthermore, in some illustrative embodiments, additional mechanisms are implemented in order to avoid undue material loss, for instance upon removing a dielectric cap material and the like.