You can set the location in Construction Settings for the part. With Construction Settings open, click the <part> Construction Parameter button at the bottom of the dialog. You have to do this for each part you wish to change and it is only for newly added holes, so you will have to remove existing holes first.
The Rafix housing is slightly proud of the edge so we need to move it inward so that when it is tighened up the joint is flush, we just need to move it away from the edge a fraction plus the hole is a little bit tight for the fitting and will need to make it slightly larger.
Use the Hardware Hole Editor. After starting the HHE, click the Open/Add button and find the hole pattern you want to edit. When you have the pattern loaded, double-click on the pattern and it will turn red. Now you can set the depth.