This took a while to figure out, so I will write it here for people.

First make sure you enable Linux developer mode on the Chromebook.

Next make sure Steam is installed and Hex of Steel is installed from Steam. Not the android app version.

Next you will need a few commands, but I will type them here for you.

Open up steam and press (ctrl+alt+t), this will open Crosh (advanced terminal program)

Next Type this: vmc share borealis Downloads
This will allow you to "see" the steam folder structure in a folder called Downloads, under My Files in the file browser (this doesn't need a special browser, just the basic one). Note, this will take a few seconds since its creating a link to that folder structure for you (like a pointer).
Do not close it until you see it start a new line in the terminal. It may look stuck, its not.

Next Type this: vsh borealis
This will enter the shell of borealis (the actual virtual machine)
Don't worry you can close this at any point and its fine.

Now is where the fun begins.
First you want to navigate to the Downloads folder that you just made available, you will see a folder called "share", that's all your steam files, but what we need isn't inside that folder. I spent hours looking through. But its still useful in general so leave it be imo.

Create a folder called MODS in the Downloads folder (not in the share folder)
This is where you will copy any mods you want to add to the game.

Any time you want to import mods to the game, or export them from the game remember to go into crosh (ctrl+alt+t) while steam is open. Then type vsh borealis.

Now to copy any mods from your mods folder (the one you made in Downloads) to the game, type the following:

cp /mnt/shared/MyFiles/Downloads/MODS .steam/root/steamapps/compatdata/1240630/pfx/drive_c/users/steamuser/AppData/Locallow/"Valentin's studios"/"Hex of Steel"/ -a

There is a space between cp and /mnt. Theres also a space between MODS and .steam

So what this says is, copy all from Downloads/MODS to the games folder location. So this will make a MODS folder if one doesn't exist and put all your mod folders into it.
Note: This will overwrite stuff, so make sure to backup, or export the mods from the game first then re-import with changes.

Now if you want to get the Mods from the game into the Downloads folder instead, we type this:

cp .steam/root/steamapps/compatdata/1240630/pfx/drive_c/users/steamuser/AppData/Locallow/"Valentin's studios"/"Hex of Steel"/MODS /mnt/shared/MyFiles/Downloads -r

There is a space between cp and .steam, and a space between MODS and /mnt

What this does is copies from the games MODS folder to our one, this is useful if you made changes using the editor and want to back them up, or so you don't overwrite them by mistake when adding new graphics.

Hope this is useful to someone, I made this solely since im modding the game myself.