Traces of fluids on the fuselage of N545JN had already been noticed and taken care of on the ground in Liege, before she was positioned to Munich. The stains were believed to be the results of a birdstrike though. The aircraft had been flying ABV- ABJ- EBB prior to coming to Liege.
Flightmech: There is an hole/opening between the nose gear bulkheads (both sides) leading into the air conditioning bays so it is feasible he could have been crushed by the retracting nose gear and got through the opening on pure adrenalin alone before passing away, but it would be very tight.
I find this highly plausible. For a small or very slim person it is doable (especially under those dire circumstances).