Reverse engineering for compatibility, and implementation of a compatible system (as long as you don't copy the original) are not just legal, they're explicitly legally protected in many jurisdictions. You'll get in serious trouble if you copy the original, but there is specific case law supporting things like emulators. See, for instance, Sony v Connectix and Sega v Accolade.
But OpenTTD is explicitly a faithful copy of the original. It replicates the original product in appearance and behavior and is open about it. If you were to dig into source code history, mailing list archives, chat logs etc. I'm certain that you could find a lot of evidence to support this position.
Show a set of random persons gameplay video clips from TTD and OpenTTD in its default settings and ask them which one of the two games they are watching. They'll be struggling.
It is about the entirety of the product, not its parts.
That's the point of game engine reimplementations, but again OpenTTD has no original TTD worlds.
Simcity 2000/3000 and Lincity-NG can look pretty close at a distance too, the same with FreeCIV and Civilization 2000.
If the issue it's due to the menu layout and such that can be set with ease, GUI presets from original TTD and a 'new' one (as default) and call it done.
Arx Fatalis itself it's a Ultima Underworld inspired clone. It's more than obvious. Deus Ex it's a weird Shadowrun retelling with better hacking depictions replacing the magic shadow ruling overlods with a panopticon AI and ripping off every US conspiracy from the XFiles.
Both RPG's can be played in pretty much the same way: half stealth/half run and gun depending on your mood, augmentations, hacking to retrieve useful info, doing secondary errands, the cyberpunk theme...
Halo does the same with Marathon and Bioshock borrows a lot from System Shock.
