I spent a night and a half to figure this out all by trial and error, some reading and browsing the web. I don't have any programming knowledge. Everything in this guide is provided as is and I'm not responsible for anything that happens to your game or your PC etc. Do it at your own risk.

1. Don't mess with the default controls.
2. If you mess up default control options somehow, delete the config.txt. It'll regen on next launch.
3. Run trupdate.exe
4. Choose utilities, download to desktop.
5. Pick TR3 contents from the downloaded file and copy the contents to root folder of tomb3.exe
6. Extract 1-3 patches to their corresponding folders and overwrite.
7. Extract voodoo's MS folder contents to tomb3.exe root folder. Choose x86.
8. Run dgvoodoocpl.exe and configure the voodoo tab.
9. From Steam app click on settings for the game and choose properties.
10. To the launch options add "-setup" without the quotation marks.
11. Run the game and configure the setup screen.
12. To set up the controller choose controller configuration from the settings in the steam app.
12. You need to have applied the voodoo's fixes to be able to use the Steam's controller configs.
Otherwise, the overlay won't work and the configs won't work either.
13. Change gama setting from the config.txt inside the root folder. Otherwise game crashes.

Mainly, what I wanted to do was to play the game with my 360 controller but the configs from Steam didn't work. Then, I learned I had to fix Steam overlay for this game before the controller configs could work but while doing that some other improvements came with it.

We will download several patches, not all are necessary just to make the controller work but are nice nonetheless. I will tell how to get them and what each one does, so you can decide for yourself.

1. Download the multipatch here: https://www.tombraiderchronicles.com/tr3/fixes.html

This fixes compatibility issues and disables CD-check according to PCGamingWiki. Extract the file trupdate.exe and run it. Choose "Utilities" in the setup and "download to desktop". Pick TR3 folder contents from the downloaded files and put the content of TR3 folder into where tomb3.exe is. You might wanna do a backup of the tomb3.exe just in case.

2. Next, download these 3 patches here: https://onedrive.live.com/?authkey=%21AEbkhytrLYjvdOo&id=F373718D7E6FEA28%21119&cid=F373718D7E6FEA28

These are improvements to sound, cutscenes and the one that says levels is completely optional. It lets you remove the health crystals from the game if you want a little more difficulty. (There are still health packs). These are fairly straightforward to apply. You need to extract, copy and overwrite them to their respective folders in the main game folder, i.e. audio goes into audio, cuts goes into cuts but levels goes into data.

3. Lastly and most importantly (this one fixes the Steam overlay among other enhancements such as fullscreen FMV videos and widescreen fix) download the latest stable version of dgVoodoo2 here: http://dege.freeweb.hu/dgVoodoo2/dgVoodoo2/

Fair WARNING before you download this. Your antivirus software might pick this file as a malware and block/delete/quarantine parts of it. Download it at your own risk. I have no programming knowledge, so I can't check the code but this software seems to have been suggested for a long time to fix old Tomb Raider games.

After you download it, there'll be a bunch of folders inside the main folder as well as an .exe file if your antivirus didn't block it. First, extract voodoo's MS->x86 folder contents to tomb3.exe root folder (where the game is). I believe you don't have to run the dgVoodooCpl.exe but if you do, you can remove the voodoo watermark from the bottom right and do some more tweaking.

Try running the game. If you have an untextured pink fleshy mess of hell, which happened to me,
you need to run the game's configuration. To do this, right click on the game in your Steam launcher--> Properties--> Set Launch Options--> type "-setup" without the quotation marks and click OK and close properties dialogue box. Now, run the game again. Setup is just a configuration window where almost everything is already set and you don't need to change them. You can change your resolution.

Now, that hopefully your game is running without a problem, close the game. Open Steam launcher and right click on your game-->Controller Configuration. You need to have your controller already plugged in for this option to appear in the context menu. Choose and apply the top-voted config. It's Leo's config at the time of writing this guide.

Launch the game and voila! You can now use your 360 controller with Tomb Raider III without any other third-party software.

1. You should leave the default controls alone.

2. If you somehow messed up the default controls, delete config.txt from inside the game folder. On next launch, it will be regenerated.

3. You can't use the Steam community's controller configurations if Steam overlay doesn't work while in the game. To fix it, you need to copy the MS folder's contents to Tomb Raider 3 root folder from the voodoo website.

4. If you change Gama setting from in-game settings, the game crashes when you try to save/load. Solution is to change it from config.txt inside the game folder while the game is closed. The default gama is too low to see switches and health packs.

5. If you get a textureless game, type -setup to game's launch options. Choose your settings and launch the game through that. In my case, that fixed it.