From your later post it looks like you own a late model Z650. The PCV in this case appears to do both fuel and ignition, so it has to physically connect to not only the injectors and TPS, but also the coils.
To be honest, all the piggy back systems are very similar in their operation. The PCV does usually have finer fueling resolution (250 RPM increments) than the Bazzaz or Rapidbike, which does make it a better choice in my opinion, but you can still do a good job with all three. A shop's preference is usually based on compatibility with their dyno and it's respective tuning software. All current dynos will have live tuning software and hardware which only works with their brand of fueling module. A Dynojet 250i will allow live tuning and monitoring with a PCV, and a Bazzaz dyno will do the same with a Bazzaz ZFi, so they can do a better job a little more efficiently. This is the reason why a shop with a Dynojet dyno may charge a little more to tune a Bazzaz unit, or vice versa. You can still tune any fueling module or flashing kit on any dyno, it just takes longer without the live tuning features.
If you have the ECU flashed at any shop, without purchasing the full flash kit, (which is typically between $500-600 just for the hardware and license), then you lose the ability to make any adjustments down the line as the actual license (BIN file) is still owned by the shop, not to mention the cabling and USB converter box which only comes with the full kit. A piggy back unit will allow any owner to make changes with a laptop should they need to, or simply re-tune the bike again if they make significant changes down the line, without being committed to the same shop. This is why you see so many race bikes with both an adjustable race kit ECU and a fueling module.
One of the biggest advantages to a flash is the ability to remove Secondary Throttle Plate or Fly-by-wire restrictions in order to allow the bike to actually receive full throttle when applied; however, such restrictions typically only appear on litre bikes. As an example, you can gain significant power by de-restricting a current R1 (fueling changes will be required as well), but no such restrictions appear on the R6.
