Kota's armor isn't mandalorian, just similar... It actually very closely resembles some of the rebel armor from Galaxies and the Jedi armor from the new SWTOR MMORPG. As for the "rebel" mandalorian part... Mando'ade are mercenaries at heart, and by definition that means that allegiances are very easily shifted. Not to mention that mandos have no love for the Empire according to any of the cannon sources. Boba just worked for credits is all.
Oh, and just a side note... the orange rebel flightsuit isn't intended for being downed on a planet and being forced to evade. It's intended for exo-atmospheric bailout. The bright color would, in theory aid in recovery of a pilot who had to punch out. TIE pilots in contrast would be much harder to find due to their black flightsuits. That being said, Rebel pilots can be noted wearing orange, red, grey and green flightsuits in ROTJ.