While the E5 is more suitable for gravel riding as rcloviere pointed out but he failed to mention that the AL 3 has the decoupler fork which makes riding smoother for the upper torso area. Also the AL 3 comes with 28c tires which means the rim and frame should handle up to at least 32c which means you can ride on gravel to some degree.
I've ridden on gravel roads on just 23c's howbeit carefully, and I've ridden gravel roads with 32's with no issues, while I'm not setting speed records, but I was doing it on a fully loaded touring bike. Schwalbe makes a low profile pebble tread 35mm tire called the G-One that should fit that bike. For some reason Trek is being a bit weird about what size of tire it will fit, they say 32 is the max but admit it could go wider, so you may want to talk to a Trek dealer.
If a person knows how to ride a bike they can ride gravel or grass on tires as narrow as 21mm which I use to do back in the day with tubular road tires, again I didn't ride fast with those but it was due to necessity; speaking of necessity I once got a way from a cop trying to write me a ticket for failing to stop at a stop sign on a mountain road, I happen to see a dirt trail going off into the woods and escaped from a ticket, I was riding on 23's at the time! So for occasional gravel road ride 32mm in my opinion are plenty good unless you want to do some gravel racing.
So if you want to have a bike that will do the road really nicely and yet do some casual gravel riding the AL 3 would be the one I would consider. However there is a twist.
The twist is that the E5 can be used for light to medium touring, it has 3 water bottle bosses instead of 2 like the AL 3, it also has rear mounts for pannier rack AND a fender whereas the AL 3 has mounts for just fenders but not racks.
So the decision hopefully for you can be made with a bit more info.