About matter:
Most often, I'd use terrain alteration to straighten an edge such that a sloped way, tunnel portal or bridge start is allowed. In reality, such operations would often be planned in such a way that removel and addition of material balances each other. The grid doesn't allow for that strategy in Simutrans, even so it makes more sense to assume it was taken into account and most terrain alterations still work that way, even if the grid-based representation doesn't show it.
It also wouldn't make much sense if terraforming operations would cause leftover material/need material, but tunnels would not.
Large terraforming projects, like removing a mountain, could be considered differently. But to do so, one would need to be able to differentiate - since any large terraforming project is nothing but a chain of tiny operations, that could be really hard.
About Energy:
As Václav said, there is deadlock potential even if you make sure there always is enough electricity on the map. Electric Energy is the one asked for most often, but if you go further and even require fuel and coal, you might end up with a map where no vehicle can move anymore due to some earlier accident that left all vehicles out of fuel or stuck between vehicles out of fuel. It could be fun to repair such a messy map by starting out with a horse drawn carriage, but it's much more likely a player would be frustrated and either load an earlier save or play a different game.
There is another aspect as well - if you need to use fuels/electricity from factories on the map, what do you build infrastructure with? Wouldn't you need a gravel mine before you can even build a gravel road? A brick factory for your first station building? How does the locomotive producer get all the materials they need to produce locomotives for you to buy and use? There is a clear separation - the player can get anything for money, no matter whether the thing can be produced on the map. Perhaps imported from some other, unseen area - who knows?
It's not impossible to think up a game where this wasn't the case, a transport-focused version of build-up strategy games like Anno, where you can't place factories and rather, factories spawn as they will and you need to transport stuff from one factory to the next not just to make money, but also to get required materials. Could be a fun game. Isn't Simutrans though.
There is a fuel idea decoupled from factory output. You'd have to build fueling stations for your vehicles to keep going, but they wouldn't actually need to be restocked with goods. -->
https://forum.simutrans.com/index.php/topic,18122