Necessity really is the mother of invention! That flywheel locker is very ingenious.
I shouldn't fret too much about flywheel balance; when I changed my flywheel for a heavier one from a Hypermotard, I noticed it had an additional hole, which is not present on the Evo's. (I think it contains a dowel or pin on the Hypermotard).
Hypermotard flywheel on right with extra hole
Like you, I wondered about balance and asked Wilf at Moto Rapido for his opinion. He said it'd make no appreciable difference and to ignore it - so I did.
I've been running it for over three years now with no problems so I'm sure you'll be fine.