>Maybe you only have sand in a desert scenario.

That is a weak argument. It is up to the scenario designer to ensure that everything that is needed to complete the level is available in the level. I.e. with the same argumentation, I could argue that lava should substitute for firestone because "you may have only lava in a vulcano scenario". Imagine the other way around - perhaps the scenario designer wants water and earth to be scarce so that it actually turns into a valuable resource!

>I could imagine other scenarios such as a new tree providing a different kind of wood that should be allowed as a replacement for regular wood.

Why should it be different? There is no need for that. You can SetGraphics your custom wood pieces if you want i.e. the "mushroom tree" wood to look different, if you must.

But, again, my argument is: What is the added gameplay value for this? It just adds complexity in code, the engine and worst, the user interface. There is the potential to confuse the player so that he does not know what to do with these "sturdy mushroom pieces" and the best that can happen is that he ist just not confused.

Remember trade simulations, like Colonization? There are various sources you get hide (fur) from to ultimately make them into coats. But there was no distinction between the different types of hide, it was just hide. And the reason was not because the developers were too lazy to make graphics for deer hide, bear hide, bunny hide, etc... but because they wanted to make clear that it is one and the same resource with one and the same properties. KISS, it is about clarity and simplicity for the user.