If a transport is destroyed in an assault but the troops inside survive, do they become valid targets for allocation of MW hits, which are allocated after normal hits? In shooting the FAQ says this is possible, so I guess it should be the same for assaults?

Assuming the answer to the above is yes can the troops, suddenly finding themselves in the midst of combat, now use their attacks? If not, they could potentially be allocated hits (in addition to the hits suffered from being inside the transport) despite not being able to participate in the assault themselves. I'm not sure how this is affected by the part of the assault rules that suggests there is no "order" to each player's attacks.

They wouldn't be allowed to use their attacks (unless another round of combat happened due to a draw).
All attacks should have been completed before either side have moved on to making saving rolls (first strike attacks is an exception). There isn't an order of which side attacks first (again first strike is an exception to the order of attacks) but both sides have to complete their attacks before they start allocating hits to units.

Think of it as them getting immediately ripped apart when they come out of their transports, due to not expecting their safe tank to go kablooey.

The yes and no consensus seems sensible, but I'm not sure it's for the reason you state here. The question of whether they get to use their attacks only exists precisely because all attacks are not completed before moving onto saves - if they were, then macro weapons would not be able to be allocated onto anything inside transports (hence my question).

Each player allocates the hits and make saving throws in the same manner as they would when allocating hits from shooting.

1.9.3 Shooting Procedure
This is a summary of the shooting procedure. We’ll work through it step–by–step in the rules that follow.
I – Place one Blast marker on the target formation.
II – Roll to hit.
III – Allocate hits, make saving throws and remove casualties.
IV – Place additional Blast markers for casualties and check to see if the enemy formation is broken.

If an attacking formation scores hits both with normal weapons and weapons with the macroweapon ability, then the opposing player must allocate and make any saves for the normal hits first, and then allocate and make any saves for the macro- weapon hits. Hits from macro-weapons can only be applied to units that are in a position to be hit by a macro-weapon
(Note: With the exception of War Engines (see 3.3.2), during
an assault, all units up to 15cm away are valid targets for
allocation, regardless of whether the hits are from CC or FF.).