all the rotary maps i have seen have been tuned in injection time, i just checked all my old haltech files and 90% of engines are tuned in VE except RX 7/8, why im not sure
hopfully simon or scott will chime in here.
Looking at your pic
Your mag has 3 spaced pickups (magnets) at every 120 deg your stock ecu can work out tdc from this but the link can not
You have the same problem we had so there was a couple of options, either add another sensor somewhere on the engine so you can run a trigger and home sensors so the link knows when a tdc event is or the way i went is making a multitooth/missing trigger wheel this worked for us no problem on our tripples.