With the same height setting on two objects, one of them is still higher.

Jakub,

As I see it,the E part and the sun part have the same height, but they have too much overlap.

The the top/bottom Anchor Points of the sun ought to coincide with the rightmost top/bottom corner Anchor Points of the E, in other words the centre of the sun ought to be horizontally aligned with the rightmost edge of the E.

Instead, the top/bottom Anchor Points of the sun are further left, behind the top/bottom segments, so we see the corners of the E being higher then the sloping part of the sun.

You ought to be able to ShiftClickDrag the sun right by the top (or bottom) Anchor Point to snap to the corresponding corner of the E.

Assuming your sun is a circle, the screenshot indicates that the red marked corners of the "E" do not match the northernmost and southernmost point of the sun.

So what you are seeing is just normal.

Your sun is round. You will have to edit the paths, so that the E is round in the same fashion.