I played Sad Sniper more times than I care to remember, both before & after trying to level of Michel. My regular levelled up michel had significantly different stats & selectable pilot skills than the one in the EX mission. The various end of mission fail screens showed a bare bones unleveled pilot, but let me max out the tune points on the VF-25G.
No matter how many times I played that mission, there was never an increase in pilot stats, nor did it show a reflection in the increase in Michel's pilott stats, or pilot skill changes that I did in other stages. Just what are you basing your assumption on?