So does the top level of a bunker provide cover? It would appear to but I do not see it listed on the card. Thank you!
That’s a good question!
The rule of thumb to follow when reading Warmachine rules is that “the rules only do what they say they do.”
EDITED TO MAKE A CORRECTION.
The specific Bunker (and Guard Tower, for that matter) rules do not say anything about cover. However, the generic Building rules in the core rulebook include the “Defensive Position” rule, which is shown below:
So, yes! Ultimately, models occupying buildings always have cover. 
(Which raises another interesting question, but I’ll save that for another thread…)
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And there is effectively little reason to put anything on top of the bunker, when placing them on the bottom floor makes them close to immortal.
You are correct, and in fact, I’ll do you one better:
I remembered this being within the Guard Tower/Bunker rules themselves, and it either was always in the generic Building rules (after they were added) or got moved there with an update and I didn’t realize it.
I looked earlier and didn’t see them on the Bunker (or Guard Tower) itself, so I concluded it had changed. Didn’t think to look elsewhere!
I’ll edit my original answer.
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Perfect!!! Ty. Problem solved
Being on the top level allows you to ignore intervening models outside 1 inch from your target when making ranged attacks.
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Easier to get off the bunker from the top if the scenario you’re playing include satchel charges which kill everything in the bunker. See: Enemy Intel Battle Forge scenario.
Bottom floor also provides elevation (for Bunker and Watchtower) due to how the rules are written.
Where do you see that?
The rules card for both specifically states “Top Floor”.
While technically accurate, it is of no practical concern, because Fortified Walls prevents you from targeting models on the lower level. 
I believe this would also apply to the ground floor of guard towers where i think that it is clearly not the intent. Wording should probably be cleaned up to say “An obstruction provides elevation to models that are on top of the obstruction and completely within the perimeter”
I have no input regarding the intent. Your best course of action in this case is feedback@privateerpress.com.