I cannot find energy consumption or pollution setting

They are in Map / Runtime settings tab, not in Startup settings . So that you can adjust it without restarting game.

For other modders

My goal is to I make MD2R maximally extensible and compatible. There are many already integrated mods, but new ones appear from time to time.

In case you have dynamically changing ore (like Tiberian Dawn), just periodically call rescan_all_depots remote interface function.
In case you have teleporting platforms (like W2 or WDM), your mod should simply ignore some entities of MD2R, by either avoiding them your side, or providing an interface to blacklist some entities' names.
In case your mod adds special resources that cannot and hence should not be shown in Depot's menu (like Deep core mining, Prospector mods), it can be easily escaped by specifying as mods-specific substring of internal ore name, see attack_proxy.lua.
For other uses, see existing remote interfaces declared in remote_interface.lua, and if nothing helps, reach me here in Discussions or on the Discord.

If you make a patch / addon (like new skins for drones), you can set both original mod and MD2R as optional dependencies. Both use the same internal entities, except drones names: they got changed from ore_name.."mining-drone"..ind to ore_name"-mining-drone-"..ind but I recommend to better use shared.get_drone_proxy_name(ore_name, ind)
If you cannot make a patch and need to fork, let's discuss, I'm open to accept PRs and expand API (remote interface functions) to allow more customisability by other mods. Btw, I already made refactoring of the original code, so it's easier to understand and change it now (and maybe will add even more refactoring).