Shell theme looks broken

I'm using a 1366x768 screen (which is quite low for a laptop) and it doesn't look right. The dock and virtual desktop bar look weird:

Icons on the app menu are too small as well:

This is how the original Yaru shell theme (from Fedora's repos) looks like on my screen:

[azumafuji]

I'm also experiencing some strange behaviour. The icons are oblong and things are now overlapping.

This is with the master branch and the yaru-deepblue-dark and yaru-deepblue themes

[Woodencross]

I'm using Yaru-Aqua and experiencing the same. The icons looks "thinner" than normal and can't align with its shadow.
I cloned the code, followed the install.sh and yes to every question in the script.

[koplo199]

Looks like a duplicate of #124, this issue is resolved in my branch if you want to test.