It’s a while since I had my hands on a 1098 but doesn’t it have a fast idle lever to the right of the left hand switch gear? Certainly the 848 I had here recently had one and that’s the same as a 1098 just a smaller cc engine.
The fast idle lever opens the throttle valves a smidgen which moves the TPS which instructs the ECU to dose more fuel making the start up mixture richer and facilitating a cold start. It’s the same as you saying you have to turn the throttle in order to get it to start but it applies a precisely measured amount of turn and saves you having to hold the throttle open until the engine has warmed up. When the lever is in use the engine idles at a higher rev than normal until you knock it off and the warmed engine can hold idle.
As for the power commander, I’m not a big fan of them. They work by piggy backing the ECU and interfering with the messages from various sensors going to the ECU to trick the ECU into dosing more fuel. Typically they are tapped into temperature sensors and trick the ECU into thinking the incoming air is colder than it really is thus the ECU, thinking the air is denser, holds the injectors open for longer at each pulse.
If your starting issue is due to an incorrect A/F ratio you’ve now got to work out whether it’s a sensor at fault or the power commander or the ECU.
I had a Panigale with me a couple of years back, was a right pain to start, didn’t idle cleanly and stuttered on acceleration. That had a PC fitted. The first thing I had to do in order to track down the fault was remove the PC from the wiring loom and go back to the original set up in order to start testing. Lo and behold as soon as the PC was removed everything was fine.
I’m not saying the PC is your issue here, you’ll never know until tests have been run, but it will be a complicating factor.