To my opinion, soldering with a hot air pencil always raises a danger of overheating because it's difficult to warm up the parts evenly. That may be different with tools that have individual nozzles for specific cases as the Weller desoldering tool, also operation with small parts is less critical.
Most companies I know are soldering QFP parts pin-for-pin with a soldering iron in prototype production (if the prototypes are not made by an assembly service provider). Also hot plate soldering is a good technique for smaller boards.
You should also consider that most QFP parts are declared moisture sensitive with a
floor-lifetime of one week after unpacking. All soldering techniques that apply heat to the complete part should follow the respective handling rules, hopefully soldering of individual pins is less critical. Otherwise, part damage by case
delamination must be expected.
Apart from this general considerations, I don't think that it's likely to get supply shorts by part overheating (it
could be anyway). I would watch out for PCB or soldering shorts first. You probably know, that FPGA VCCINT core voltage pins have a low resistance to GND without a supply voltage.
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