1.apothecary rules are quite clear-i failed armor save per player turn is igored as long as the apothecary is not locked in CC and the wond does not come from an instant death double toughness weapon. a terrain check is not a failed armor save so therefor the apothecary won't help you.
2 you always take a terrain check when driving through terrain including assaults into terrain which now makes bike heave RW armies the suck without skilled rider.
3.i prefer 2 flamers per bike squad for dealing with low T /weak save units hugging cover like IG or eldar scouts