its runs fine i wouldnt worry about it, but its clearly not optimised for it.. Much in the same way as if you drop a 1.2 8v spi into a cinq you usually just use the 1108 factory ecu, it works just fine but they run better on the actual p60 ecu.
I've been in a few 1368 16v centos running the 1.2 16v ecu and they all seem to have this hesitation if you go from really low revs to wide open throttle instantly but you easily learn to drive around it. Once you are going along it doesnt do it and runs perfectly fine. Perhaps swapping the cams will help i dont know but its certainly worth swapping them if you have the early 1.2 cams.
The other option using all factory parts is to use the 1368 ecu, this does mean a few extra steps though obviously, you obviously would need to fit a fly by wore throttle pedal. I don't know for sure if that ecu needs all its canbus modules plugged into it to work, you'd have to do some research. And of course the wiring won't be as simple being the loom on a cinq/sei spi is almost identical to the mk1 punto 16v one.
I know I have seen one cinq with the 1368 ecu and it had the dash cluster and the buttons from the middle of the dash fitted badly into the cinq as well - but I'm not sure if it would work or not if you spliced the loom into the sei so the factory dash worked or if the ecu would throw a paddy about the other modules not being plugged in, sure the info is out there i just don't know without looking. This is a genuine issue with newer cars and engine swaps though - i know for example if i were to tjet swap my panda 100hp I couldnt use the factory tjet ecu because it will not run without all the canbus modules from the donor car and I'd want it to look as factory as possible and so the only real option is an aftermarket ecu
makes it alot more hassle and alot more expensive to do annoyingly.
But if i were to do another 16v cento swap I think I would stick to the early 1.2 16v ecu way (IAW 18.FD is the ecu if i remember right, been a while). But I'd consider getting a piggyback like a DET3 on it so it could be optimised to the exact setup of the car, they are pretty cheap and powerful for what they are.