It is not the base but the actual model that determines if unit hiding behind hgets a cover save; you use real Line of Sight, so you get down and see how much of your target is behind the intervening model. In the case of a Hive Tyrant being obscure by Gargoyles, that's perfectly allowed and an oft-used tactic to give your Flyrant a little protection. As for modelling for advantage, there is no rule against it but it generally is frowned upon. There's no cut and dry way to distinguish between acceptable levels of MFA(modelling for advantage); that is to say, there's no technical difference between you constructing your Gargoyles with their wings spread wide and at different heights and an IG player making all his infantry lying down to make sure they always get a cover save. The best way to avoid unpleasantness is to ignore gaming concerns when making your model.
"Trying to make some sense of it all,
When I can see it makes no sense at all"
"Fools to the left of me,
Jokers to the right,
Here I am,
Stuck in the middle with you."