Difference between using ⌘ - space vs 'open -a' in terminal?
The problem you are having is a constant for Emacs. It's due to Emacs relying on a couple of things that are set in a bash shell that aren't available in the GUI.

The most notable of these is the PATH variable. That's why pdflatex isn't being found.

Check https://www.emacswiki.org/emacs/EmacsApp for a better explanation and some things you can do to make it easier.