The "not enough pins" is probably referring to the older Aqualink PCBs only having one dedicated RS-485 header which - in your setup - is currently occupied by the PDA Jbox connection. The revised boards, including iAqualink, have 2 (plus an RJ11 port). However, you can put multiple devices on one RS-485 header, so I'm not really sure what he's talking about. As long as your current firmware is new enough to support a variable speed pump, it should be able to be connected now and work properly. But at the end of the day, the Jandy PDA solution is still hot garbage. IMO, I'd just remove the PDA part altogether when you upgrade, it's useless.
Upgrading to the iAqualink will get you the new revised PCB and it'll fully support your new VSP and allow you to use the mobile app.