The Joe Blow Pro has Topeak's Smarthead, a dual Presta/Schrader chuck. It has to have a pin to depress the valve when used on Schrader valves, therefore I would argue that it is designed to work that way. In fact, if you look inside the Smarthead while you operate the locking lever, you can see the pin move slightly towards the "front", i.e. towards the valve.

If you don't want to lose air into the hose (air escapes through the open Presta valve and pressurizes the hose up to the pump's check valve) then you don't insert the Smarthead as far onto the valve. However, some Presta valves are "necked" down a bit at the end making this tricky, and sometimes the chuck will come off the valve when trying to pump the tire. The Presta valves that Shimano supplied with my Dura-Ace 7850 tubeless wheels are this way.

If the idea of the Presta valve is to prevent any air loss when you insert the valve (more important with an "onboard" pump than a floor pump) then tapping the valve stem before inserting the chuck defeats that purpose, doesn't it?

So back to the OP's original question, perhaps his Smarthead is worn. Or he can ignore it, unless of course it doesn't work when he tries to pump a tire with a Schrader valve.