Shaken, stunned, weapon destroyed, immobilised:
At the end of the phase in which a vehicle sustains one or more of these damage results, the passengers must take a leadership test. - It then goes on to talk about the consequences of the test. Interestingly enough fearless units will be subject to this test as well
That's because Leadership tests and Morale/Pinning/Fear/Regroup etc tests are not equivalent. Fearless units automatically pass the latter, but may be required to take a leadership test by various effects that have some consequences.
As for the actual question you posted, the rules say that every penetrating shot must roll on the vehicle damage table as well (it goes on to say that this is because you could still get an explosion, but it doesn't in any way invalidate the other possible results). So my view on the matter (and how we have played it, is as follows:
1. You score two glances
2. You score a pen hit. This takes the last HP, but the rules say you still have to roll on the VDT. You do that and get a stunned result.
3. The rules for transports suffering damage say that whenever the vehicle sustains such a result the passengers will take a Ld test at the end of the phase.
4. The effects from losing the last HP apply - the vehicle is now wrecked and the transport rules kick in again. The passengers must immediately disembark and take a pinning test - if you fail you GtG. The vehicle is afterwards considered a wreck.
5. The end of the shooting phase comes and you take a Ld (which is not a morale check but it doesn't matter anyway as pinned units are still eligible to them) to test on the survivors because of the stunned result.
You take two tests total - one which is resolved when the vehicle is wrecked and the other at the end of the phase. I could find nothing that invalidates this order of events, though as always I may be wrong.