Has anyone tried to get conformal coating under a BGA? (large package MPC555). There is a concern with ionic/metal bridges developing between contacts due to accumulation of dust/humididty. Final product is Class 3 (aerospace).
Your dust collection / humidity / ionic path concern is reasonable.
Consider applying your conformal material thick enough to form a good barrier between the device edge and the board, similar to what you do for QFP. [Admittedly the QFP is not a precise analog, because there are not bare connectors, except maybe via under QFP.]
Thinning and applying conformal material under BGA is a very dicey operation to control. It can be done though. Alternately, if you really need material under the BGA, consider an underfill, similar to those used for flip chip. Be aware of potential Cte issues when selecting materials, since package designers select materials for plastic BGA so to not require underfilling.