I just spent way too long trying to get alt Enter to launch a terminal with my ~/.Xresources. When I finally tracked it down I realized that this isn't strictly an i3 issue, but if you're hitting this hopefully this will help you troubleshoot.

First, i3 comes default with a wrapper script for launching the terminal called i3-sensible-terminal which depending on what OS you are using makes tries terminal emulators in order until it finds one that works. https://build.i3wm.org/docs/i3-sensible-terminal.html

This, in itself, is fine. I knew that Debian used xterm and I went about setting some configuration in ~/.Xresources. Nothing happening. I ensured I had run xrdb -m ~/.Xresources... nothing. I checked that my settings were loaded xrdb -q Xterm. Yep, there they were....

In short, Debian also has a terminal wrapper that by default sets a new class with which to configure .Xresources.

-class UXTerm

Long story short, if you're reading this and it seems like your .Xresources never get loaded run a ps faux | grep term and see if you are using the right class.