Greetings,
The primer depth is controlled by adjustment of Item #44, Primer Punch Push Rod.
Set the adjustment so that the primers are at least flush with the end of the case.
Call the manufacturer of the primer and ask what seating depth is recommended. Some say flush, others say -0.003".
If you use brass of various head stamps, this adjustment will be hard to control as each brand have primer pockets of different depths.
Back to your original question, yes, the punch "may" rise above the #26, Primer Punch Bushing.
Cheers,
Dave Wilson