In my opinion, this is far preferable - you still have engine braking as normal, but because there's much less, the throttle feels way less twitchy ('on/off'ish) when you're at high RPM's. The flash by default (you can have them leave it on if you like) disables this, so idle-level fuel injection continues under deceleration. The hard engine braking on the MT07 is due to the engine cutting fuel injection completely under deceleration. Throttle response feels significantly better specifically when you're cranking it open. There's some gains to the midrange too, but it's less noticable as the midrange on the MT07 is so strong even bone stock.
It runs substantially better at both low RPM's launching and particularly at high RPM's. Now, I ride like an asshole, and I absolutely explore the full power of the bike every single day, but it's more than just power. I got a 2WDW tune on mine after installing a Black Widow 230mm full system and yanking the snorkel, and holy hell did it ever make a huge difference vs.
If you're changing the exhaust and intake, then yeah you definitely need to have the bike tuned in some way, but even if not?