That is definately a lean burn down that occurs when the combustion chamber temp exceeds the melting point of the piston. Hottest part of piston is the exhaust side thats why its melted away down to the top ring.
Vipers have a lot of timing advance in the cruising RPM range at part throttle. The more timing advance a sled has the hotter the piston gets...reducing ignition timing transfers heat into the exhaust.
Low octane fuel increases combustion chamber temperatures and also has little resistance to detonation that can damage pistons and rod bearings.
Water in fuel can cause jets to ice up and lean out the fuel...ethonal fuel usually has fuel suspended in it as it is hygroscopic...really bad for our two strokes.
The exact cause of your centre piston damage is likely a combination of the above items and the perfect conditions for the damage to occur.
There has been a lot writen over the years about Vipers and avoiding piston and crank bearing issues, some you have already done.
Some items that can be done:
-check and elliminate any airleaks
-run oil pump setting on rich end of adjustment...you want to be using at least a quart or litre per tank of fuel
-keep carbs clean
-run premium fuel only
-add a SRX rear cooler for better cooling[helps keep heads cooler]
-add "opticool" head gasket for better cooling
-add SRX base gasket for better cooling
-head mod to even out compression...Vipers heads have varying volume between the cylinders...match all three to the LARGER volume one
-raise the carbs needles
-jet main jets to Yamaha's jetting charts on the conservative side
-run the stock pilots and fuel screw settings
JM.02c
Bob