I've put in a LOT of travertine and tumbled marble on backsplashes. With the inclusions, it is recommended to grout over everything. Yes, this fills the holes....but if your grout is a similar colour as the tile...it looks great, and doesn't collect stains, food bits, bacteria, etc.
Avanti Tile & Stone
The most damaging phrase in the English language is: "It's always been done that way."