First, the simple one, I'm talking about the gray box where the textbox is, that box is not the same height as the same gray box of the middle panel (middle and left panel wave the same height). If this is not clear I'll send another image...
Now the "folder icon" issue....I understand the confusion. Let me explain:
On the left panel, I have a tree estructure of directories, I can go deep inside until I find the file I want to work on. In this part of the IDE I like to see yellow icons of folders (not flat, by the way) And this could be an option to see them or not (so everyone is happy)
But in the breadcrumb, I don't feel the need to se that icon because it is another way of representing the parent(s) of the file. Besides, without them we have more space to show more breadcrumbs
And as an example, let me show you how windows 10 manage the same scenario