There are a few things you can do with the tune, but from the original post mentioning a tuner, the wise move would be to take him for a drive so he can view your concerns from a real life perspective.
With aftermarket ecu's there are over run settings which can adjust the rate of deceleration and to what revs it disengages (starts firing the injectors again). Tipically (OEM) and for emissions reasons, the injectors are fully shut (all fuel cut) in overrun and to pass emissions this needs to happen within 2 seconds of throttle shut. This is all good for an emissions (and fuel economy) stand point, but can have adverse effects when sudden drops (clutch in) cause a lean condition and the engine has a hard time adjusting.
What has worked for me is to run the lower rpm ranges with a percentage (1-3%) of fuel back in the system. With 'simpler' ecu's this may mean turning overrun off around 2krpm and using a lower than vacuum (around 17kpa) tuning row to drop a little fuel into the tuning map. This has 2 effects, there's a little fuel in the chamber and settles the idle cells earlier (keep the values around idle consistent) and keeps the cylinder chambers cool (racecars use nearly no overrun and is why you see flames shooting out, but that kills mufflers and cat converters in no time). Also adding in a degree or 2 of timing on the lower vacuum cells around idle will help with the dip, but may create oscilations in the idle if too agressive.
If it is a recent event and the car ran fine before, you probably have a vacuum leak. The most common places are any hoses near the IM as they are subject to the most abuse. MY pcv valve on the rocker cover took a dump soon after I started boosting and the idle was affected (as well as the dipstick, it continually blew out and hit the bonnet).
Hope this helps
