Ok lets put it another way. In a perfect world when tiling Bathrooms etc, i prefer to
tile the walls and floor without any sanitary ware fixed (except bath and shower tray. There by all sanitary is fixed after tiling. So the order of the job would be,
Bath and shower tray
Tiling
Grouting
Fix of sanitary
Silicon.
This would mean as you say the Silicon would be on the grout as opposed to being in the joint. Personally i have never had any problem due to this in over 30 years.
Most failures in the Silicon dept are down to not applying to a clean dry surface in the 1st place.
When smoothing the Silicon to get the finished look i prefer to apply the Silicon using a suitable mitre on the nozzle and to make sure the Silicon is pressed very lightly between the 2 surfaces. Then i use a wet finger either moistened with saliva or a weak mix of washing up liquid and water. For the final finish i like to spray the Silicon with a fine mist of washing up liquid and water and tool over with a rubber finger or the like. I guess what ever works for you is best.