Top down shooter with multiple height levels

Leave projectiles with natural shapes, and check collisions with appropriate invisible proxies in addition to the actual objects.

For example, a cylinder (or, in general, a prism) extending above a level 0 building, spanning the whole height range of level 1, lets the building be hit by horizontal shots fired at level 1 (but not at level 2 further above).

Well, I already added a long collider. I've added 3 screenshots of my current prototype.

This is a screenshot shortly before it hits the first "building". In the top-left view you see the scene from top above (orthographic view) while in the right window you see the actual game view (perspective).

It's already quite visible what's wrong. In the right one, the laser shots are already at a position where they should get triggered and do damage to the building.
[attachment=7415:perspective1.jpg]

Next one shows the first frame when the shot's collider hit the buildings collider. The scene view shows the view from the side. As you see all 3 colliders of the laser intersects with the building. Works so far. However, the problem is that in the game view, the laser is far inside (top of) the building) so it causes quite some strange perspective. It gets even worse, when a ground unit shoots, so the laser offsets are quite significant.

[attachment=7416:perspective2.jpg]

Same as the above, just with top view on the scene
[attachment=7417:perspective3.jpg]

Technically I'd have to make a cone-like collider (the middleware I'm using, Unity3D, only offers Cube, Sphere, Cylinder, Mesh and Wheel (for cars) collider) to correct this perspective. Even though I doubt that would fix the problem when it's fired from ground position.

Someone ever had to solve this kind of stuff in an top-down shooter?

So you'd like to check collisions in screen space? In the first screenshot, the bullets should have hit as soon as they are drawn over the dark red faces?
You could project relevant faces of the building (the footprint at ground level?) and the projectile onto the screen plane, with the same transform you use for the camera, and check for a 2D collision.