For clarification for all, I didn't undo the linkage for 1 reason, easier to go back to using it in the future if desired, and it simply doesn't need to be disconnected.
Regarding the time and check engine light, Alain has not responded, likely because he added "disable ISCV" option to the software, just not in your tune file for some reason.
I'll have a look at correcting it myself tonight since I saved your tune.
Regarding secondary throttle open/close positioning etc:
It serves one purpose, and one purpose only, to limit power. The ECUs very rudimentary control strategy doesn't account for closed throttle over run, cold start, altitude, airflow variance due to harmonics, it's literally there so Triumph can nanny you in low gears, that's it.
It doesn't help, or hurt, power delivery in any measurable way using stock cams.