Can't think anything how connecting a scanner would affect engine - T6 even has a gateway between OBD socket and actual CANbus.
How long is your ownership? How many miles?
Any backstory before/during your ownership re EGR, DPF, AdBlue?
Please check exhaust tailpipe - is it sooty?
Any chance you could make a couple of engine blockmaps under varying conditions = while driving - by using VCDS "Repeats" option.
Please keep cabin heater blower at speed 2 or above - to eliminate "smart charging".
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Each blockmap takes 1 minute 6 seconds - thus adjust "repeats" according your journey. Minimum of 20 minutes would be nice. Ideally then 1-2 blockmaps hot engine idling at the end of the journey.