So, whenever you check the 'ignore collision' box, that specific tile, will NOT be read during the collision checks, because, by default the highest tile( the one that appears above all other map colliders ), is the one that gets used for collision checks. I.E. so if the trees branches from the above example, has NO collider attached to it, and the rock behind the tree has a collider, without the ignore collision flag checked on the tree's branches, the rocks collider will be completely ignored D: but WITH it checked, the tree's branches will not be checked, and instead it will check the next lower layer instead, in this case the rock behind ^^
Hopefully that's a bit clearer sorry I'm bad at explaining haha ^^;