All i can say is. How many times can you guys screw up.
An atlas, (and indeed most mechs), have significantly thicker arms, legs, and much deeper, (i.e. frnt to back thickness), torso's than a human that size would. Trying to scale a human upto atlas size and saying that proves the atlas is denser than water is total mathmatical nonsens. But then so is using the OP's shoebox design. Lets see if we can't do better.
Usinf MW4's atlas model, (it's easier to get specific angles than the wiki image's odd angle), it is roughly 3 times taller than it's total torso width. It's legs are slightly under half the width of the torso, and the arms are about the same size as the legs. The head proportions are about right. Thickness wise it looks to be about 0.75 times the torso width, but lets go for 0.5.
For myself these meashurment are about a quater my torso width for arms narrowing to less on the lower forearm, except at shoulders where natrually they're a tad wider, legs are a littile smaller, (maybe 0.35) at the thighs as they are quite well built, and about 2/3 that on lower leg. Hieght to torso width is 4 to one instead of 3 to one.
Obviouslly getting any kind of meaningfull figures out of this is hard, i'll try my best using 13M base height and ignoring the head.
Torso highet is about 1/3 total. That gives us 4.5 meters as the width ad height, and say 2.5M for thickness of torso. Arm's are about 2.5 M and the upper forearm is to the bottom of the torso with an equivelent length/thickness forearm. Legs are about double length of torso.
so that works out at:
Legs and arms:
2.25^2*9*4 (all four limbs), 182.25m^3
4.5*2.5*4.5 (torso), 50.625m^3
Total 232.875m^3
Density: 429.4KG's per m^3
Just under half that of water. Now square cube law being what it is and a fair bit of fudging being involved there's room for variation on that. Not to mention 50 diffrent depictions. Overal however it is going to be very hard for such a miss-proportioned mech to come relmotly close to human densities, it might be barely denser than water, but thats a push IMHO. I als don;t buy the percolation thing, the armour supposedlly incorporates a self sealing foam layer for water and space oporation. Why have that if it's not waterproof anyway.
Of course this ignores the whole reality of it. Namely a group of people with no idea of scale drew the thing up using virtually zero knowlage of any real science. It dosen't really have to be workable, just look cool

.