how much difference does it make?
it's debatable. you can do more with the flash than you can with a piggyback system such as a power commander.
not only can you modify the fuel mapping you can adjust things that yamaha made adjustable in the ecu.
some bikes have more than others. but some examples are fan temp adjustment when it comes on and goes off. you can change what rpm the upper fuel injectors start working, what rpm the intake track changes length. ignition timing, turn off the trouble code warning light for the exup valves. and a few other things I can't remember. some of the newer bikes 2017 and up you can use the flashing software for diagnostics. since starting in 2017 the euro 4 emissions put a stop to the bike having a built in diagnostics. (thank europe not usa for ruing the bikes).
I chose to buy the flash kit myself. now I can run a auto tune at any time and change the fuel mapping. or make any changes I want to everything else. which on the R1 is a lot of stuff. I went with woolich because unlike FTECU you don't need internet access to use it. (dumb as hell move FTECU).
so keep that in mind if you go with ftecu, if you're at a track and have no wifi you can't do anything to your bike. especially if you're having some kind of issue and need to change the settings. you're shit out of luck.
so long story short, yes it makes a difference. will it make your bike gain 10 hp? no. could you theoretically gain 10, yes as long as you know what you're doing and have access to a dyno.
however, there is a risk with flashing a ecu. not many people have problems but it has happened. some yamaha's have a immobilizer anti-theft system. if it locks up it bricks the ecu while being flashed. a company in england used to advertise they can fix the ecu if you brick it. I don't recall their name.
some guy on this forum bricked his ecu on a 2004. I honestly never heard of a 2004 being able to be flashed so it may be riskier to try it to ones below 2006. I have a 2015 R1 and it didn't flash properly once. the bike would not start. I flashed it again and it was functioning normal. so it can happen and it can **** it up.