Either way you will need to secure the tower to the bar. If you bring it up through the bar top it will look cleaner but then you need to secure it with anchors which will not be exposed on top of the bar. The tower will also be shorter than stock.
Flange on top of bar will require either anchors in the granite or coring with a hammer drill with the appropriate size bit. If you have not cored granite before, you may want to have a professional perform this.
Scott Zuhse, Instructor
Micro Matic Dispense Institute