It depends on the inclusions and the species of stone. I fully understand your point. If you have a strand of top amethyst and there are a few in the mix with large veils or phantoms inclusions they will definitely detract on the continuity of the strand and must be removed. One can expect this from time to time and either plan accordingly to have them removed or placed inconspicuously at the back, or buy extra to replace them.
A high quality setting and necklace requires consistency.
However many mineral stones are not so pure. Tolerance for such may be prudent, and a great deal of latitude is required. Some fine opaque Sugilite can be had for a hundred dollars a strand, up these to clear deep fuchsia/pink gel of Pure Manganoan Sugilite Silicate and you can add a zero to that number. Its to a certain degree matching the grade of stone to its application.
Also some stones would be no where without their inclusions, Rutilated Quartz, the Schiller in Oregon Sunstone, A degree of Jardin in Emerald, Tourmilinated Quartz, Fine Jaspers, Sagenitic Agates, Banded Agates, and Moonstones.
And every customer is different as to their expectations and desires.
Keep the strands/cabochons consistent and appropriate to the piece and cull the ones that arent up to par for the particular quality level in your specific project.
