1) I activate bait doll on my opp's face down mst
2) mst is force activated but being a spell it has no effect and is flipped face down
3) AFTER its flipped face down by Bait Doll, my opp' decides to chain the mst to destroy my Bait Doll, destroying it and stopping it from returning to my deck.

now my question is, since the second effect of bait doll (flipping spells face down) has just resolved, wont Bait Doll have already returned to the deck and gone out of the jurisdiction of MST's Effect?

Bait dolls effect will still be played because it wasn't negated. So it will shuffle into the deck, and mst will be gone because they wasted it.
Example, you activate card destruction your opponent chains mst to destroy it, but you still get the effect.

Yes, i know it doesnt negate anything. i was asking, if it destroys bait doll before the effect resolves then will bait doll be shuffled back into my deck?

It does, thanks alot

Yes, we established that yesterday, but thank you anyway.

Ok, let me rephrase that. I established that yesterday after i read the official ruling and thought about it for a hour or two (3 days without sleep sucks)