Mandolin bridge setup (also applies to archtop guitar bridges):
 

Above is your basic adjustable bridge. We assume its feet have a vacuum fit to the top under tension.  A vacuum fit is essential to good sound transmission.
 

Here the top is lowered all the way. Note the remaining clearance under the center of the top of the bridge. 
 

What can you do to lower it further? Well...it would be best if you didn't have to do this, but if you are careful, you can cut away a bit of ebony from just above the thumbwheels so the center of the bridge drops lower and touches the base, like this:

I've left a white line in this sketch to indicate there's a seam, but in fact the wood is touching wood. The thumbwheels are now little more than a decorative element. The point of cutting underneath is to preserve the intonation profile on the very top where the strings make contact.

If doing that means it's still not low enough, you can now begin lowering the top, which will entail recutting the compensation setbacks for the courses, and recutting grooves for the strings.

This is semi-quick and dirty, but it works, and has less of a deleterious effect on the volume than you might think. A lot of Flatiron A-5s have this issue - a less-than-ideal neck angle resulting in a bridge that can't be adjusted quite low enough.

Ideally, you would reset the neck so the bridge could remain tall and adjustable and the top structurally strong.

Let's look at this issue again. 

If the action is pretty close when the bridge is adjusted down fully, you can lower the top a bit by cutting the bridge top under the wheels. If it becomes too thin, the string pressure will overpower the wood and it will crack, making the bridge swaybacked and useless:

At the very least, a reduced bridge top will not sound very good. And if you later have to raise it up to correct the action, the string tension increases, and the top is even more compromised.

If you can keep enough wood above the thumbwheels, it's possible to take a little bit off the underside of the ebony above the wheels to exert slight pressure on the outside of the wheels themselves, like this:

This is an exaggeration, but the yellow space is what I am talking about. Mandolin bridges have a tendency to settle in under the enormous string tension they have to bear. The top flattens, the center sags a bit and the outer ends of the feet naturally tend to lift. This tweak will help keep the feet down and snug against the top. If you overdo it, however, it will make the bridge top crack, as above. 

Don't underestimate the string tension!

The ideal situation is to leave a good bit of wood in the top (or saddle) of the bridge - it transmits sound better, and it won't sag.