e.g.
$a = Real(0.00001);
$b = Real(0.00002);
$a == $b should be true with the tolerances you set, whereas
$c = 0.00001;
$d = 0.00002;
$c == $d should be false.
I believe the answer to your question is yes. When comparing MathObject Reals it considers them equal if they are within the tolerance. Be careful that this applies to MathObjects, but not perl variables.