I'm running Prey in Linux and the base game is running, however I can't get the DLC Mooncrash to install as it can't detect the base game. Tried running in WINE and using Gamehub but no luck and can't find anything online. Any help would be appreciated.

I'm not a Wine guru, but have you pointed it to the same folder as the original install? ie. WINEPREFIX=<original folder> wine <other installer.exe>

I just picked up the bundle and will be giving it a go soon, just trying to work out where the DLC download is myself.

EDIT: The trick to finding the DLC was to scroll down... carefully hidden :)

Update: Went through the install, did a brief test with the base game, and then installed the update. It comes up with an option to play Mooncrash now, and knew where the game directory was during the update.
I had a little more fiddling to do as I was using Steam Proton.

If you're using a wine game wrapper program it may have an option for running the DLC installer directly in the prefix, so have a look around in it first.

If you're using relatively straight wine first find your prefix directory:

$ find ~ -name "Prey" -type d
(ie. look for a directory called Prey inside my home directory)

On my system I found:
/home/myuser/.steam/steam/steamapps/compatdata/Prey/pfx/drive_c/users/steamuser/Saved Games/Arkane Studios/Prey

The WINEPREFIX is whatever's before "drive_c"
So my WINEPREFIX is /home/myuser/.steam/steam/steamapps/compatdata/Prey/pfx/

Make a backup of the prefix folder (cp -a, or cp -a --reflink=always if you have BTRFS), which will be many GB if the installer installed to drive "C"

Then try launching your updater pointing to the original game prefix:

WINEPREFIX="<your prefix>" wine "<path to the DLC installer.exe>"

Hope it works for you.