The fat will affect the final product if you turn it inside and it contacts the salami. I have found that the fat will adhere and dry to the salami so that when you go to pull the casing off the finished salami, the fat remains stuck....and very difficult to both identify and remove. Most times the fat has off flavors. For this reason, I put the fat on the outside.
On the other hand, the Italians have traditionally done the opposite and put the fat on the inside. Reason #1 being what was inside the casing when the animal was alive....and the potential pathogens that could affect the salami.
Keep in mind that they old ways, they used fresh casings so no off flavors when the fat dried. Also, they did not use starter cultures and relied solely on natural fermentation methods.
Making salami the modern way, we use starter cultures that create bacericides that act like antibiotics to help inhibit bad microbes. We also can flush the casings with vinegar solution. For these reasons, I have no fear inverting the casings and putting the fat on the outside....Oh- and using mold 600 also will help kill off unwanted pathogenic bacteria on the casing....