Thanks again for all the input.
Digging through some pool paperwork left behind, the Intellitouch controller was installed with the pool, filter and heater in 2007, along with a Max-E-Glas pump, I'm assuming it was a single speed pump.
In Jan 2020 the Intellipro VSF pump, Spa side remote and the "Intellicom II Intelliflo interface for automation" was installed, all on the same quote. Could it be possible that at the time of installation in 2020 the 2007 Intellitouch could not control a VSP so they had to add that module? If that's true, then why does the Intellitouch seem to have options for pump speed? Could the addition of the Spa side remote required the Intellicom module?
Went outside to get a better idea of the wiring:
From the attached picture below, from the Intellicom module to the i5 board:
Program 1 red and black twisted pair - to FLTR PUMP on i5
Program 2 twisted pair to - AUX 4
Program 3 twisted pair to - SPA
The COMM port on the Intellicom red and green appears to go to the pump through the thick black cable - would the pump only need two wires in the RS485 connection (pump has a separate power conduit attachment). The blue and red from Intellicom COMM port appear to be wire nutted together to the comm port on the 520076 board and wired with both the spa remote and Intellitouch- white being the spa side remote and the "bottom" blue going into the house. The "top" blue cable is attached to the GAS HTR port on the board, and indeed, goes to the heater!
At this point I am going to let this mess rest until something is really wrong with it, and just adjust time/schedules with Intellitouch in the house, and pump speeds at the pump.
But it remains curious to me why they would do it this way, since it appears the Intellitouch should be able to send a variable speed signal to the pump.
Thank you again -everyone- for your time and ideas!