First, you cannot fit a NovaMega sleeve into an RB/Nova crankcase, because, the locating pin on the crankcase is on the exhaust side on RB/Nova and on the Boost port side in the case of the NovaMega, don't know why, but MS has assured that in a Mega, only certain original spare parts can be fitted.
You can fit it if do a cut on the sleeve and pray for doing well at the first try and have all the ports correctly located in the channels of the crankcase.
Regarding crankshaft, you will lose performance, RB has been quite agressive on the timing of the Rody units (are balls out race engines, not for the puny).
A full circular crankshaft can have some advantages in the case of guiding fuel to the ports, as the trailing part of the crankshaft still squirts fuel and air to the ports, but have to have a correct cut to do this. Rather than this, I don't see more advantages unless weight wise, S1 and MicroCasted pistons (NSR/RR models) are slightly lighter and creates a little more shake on the the engine at certain speeds.
This last cannot frighten you, is IMPOSSIBLE, NO MATTER WHAT they told you that a monocilinder engine is completely balanced unless have some counter rotating axle that removes the shake, you can adapt a little the weight on the bob of the crankshaft, but you need to have at hand some kind of crank balancer and isn't a readily available machine unless you have at hand an engine shop. But CANNOT BE COMPLETELY balanced, you're forewarned.