Why doesn't FullSimplify drop the Re function from an expression known to be real?

The problem is due to Mathematica thinking that the version with the Re[] is actually simpler. This is because the default complexity function is more or less LeafCount[], and

In[332]:= ArcTan[-Re[x+z],y]//FullForm
Out[332]//FullForm= ArcTan[Times[-1,Re[Plus[x,z]]],y]

whereas

In[334]:= ArcTan[-x-z,y]//FullForm
Out[334]//FullForm= ArcTan[Plus[Times[-1,x],Times[-1,z]],y]

Here is a function that counts leaves without penalizing negation:

In[382]:= f3[e_]:=(LeafCount[e]-2Count[e,Times[-1,_],{0,Infinity}])
{LeafCount[x],LeafCount[-x],f3[x],f3[-x]}
Out[383]= {1,3,1,1}

If you tell mathematica to simplify using this complexity function then you get the expected result:

FullSimplify[ArcTan[-Re[x+z],y],(x|y|z)\[Element]Reals,ComplexityFunction->f3]

Out[375]= ArcTan[-x-z,y]

I think this is a bug.

Close enough expressions yield better results, e.g.

FullSimplify[ 
             ArcTan[ -# Re[x + z], y], (x | y | z) \[Element] Reals
            ] ===
             ArcTan[ -# (x + z), y] & /@
  { 1.0,   1, Sqrt[1.], Exp[0.], 1 - 0., 2, a}

{True, False, True, True, True, True, True}

The problem seems to be specific for a factor -1 before Re[x + z], other factors appear to give what we would expect. If there is ArcTan[-a Re[x + z], y] in the expression it works well. It should be noted that the same issue comes with Simplify and that the problem has nothing to do with ArcTan, because :

(FullSimplify[-# Re[x + z], (x | y | z) \[Element] Reals]
         ===  -# (x + z)) & /@ 
  { 1.0,  1, Sqrt[1.], Exp[0.], 1 - 0., 2, a}

{True, False, True, True, True, True, True}

To fix the problem you could use e.g. Refine instead of FullSimplify,

Refine[ ArcTan[ -Re[x + z], y], (x | y | z) \[Element] Reals]

ArcTan[-x - z, y]

Edit

Another way to deal with similar expressions wolud be hiding a minus sign into Re, e.g.

Re[-(x + z)] instead of -Re[x + z].

Sometimes a more flexible way would be some kind of replacement, i.e. setting ArcTan[-a Re[x + z], y]] wherever in expr one finds ArcTan[- Re[x + z], y]] and then expr /. a->1

FullSimplify[ ArcTan[ -a Re[x + z], y], (x | y | z) \[Element] Reals] /. a -> 1
FullSimplify[ArcTan[ Re[-(x + z)], y], (x | y | z) \[Element] Reals]

ArcTan[-x - z, y]
ArcTan[-x - z, y]