The Steam version does not have a stand-alone link to the setup program, so you'll need to do a little tinkering.
Once the game is installed, follow these steps:
Instead of fast quitting with Alt + F4, be sure to save the game and quit through the menu at least once. (That is, while playing press P, choose Exit to Title, press Esc, choose Exit.) The game should "remember" your settings for next time. You can then repeat the steps above and remove the " -setup" from the Launch Options box so you don't have to go through the setup every time you play the game.
Also note that if you have a widescreen monitor and want actual widescreen with no distortion, you'll need to use a player-created patch, since the game was designed to run on standard aspect ratio monitors. Follow this link for Mr. Fourblack's classic Tomb Raider widescreen patch.
UPDATE: 9/28/17 - Thanks to Weslei for helping me update these instructions.
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