If it's only popping on shifts, it's probably just retarded ignition timing at low airflows, with no additional fuel injected. COBB Accesstuner doesn't have the ability to tune these engines for multiple injection events, or to disable deceleration fuel cutoff, unless I'm unaware of changes from the FA20 to the FA24. My FA20 also afterfires sometimes on downshifts, due solely to the idle ignition timing being retarded.Would any pulsing on the overrun to create a "burble" lead to drastically higher fuel dilution? I know I have two sets of final run files that my tuner provided me with, one burble tune and one normal. I believe I have the burble tune loaded now. FYI it is not as aggressive as say a stock Elentra N is but it will pop some on redline shifts and some cold downshifts.
In any case, even if fuel is being injected during deceleration, it won't cause much dilution since it would be a small amount of fuel and it wouldn't be injected when the piston is low in the cylinder. It probably wouldn't be doing the catalytic converter, turbo, or O2 sensors any favours, but I'm not sure if it's known to cause any issues.