Is there an option to disable some of the mods that are included in this(mineclone 2) subgame?
No. Not without editing MineClone 2 itself, that is.
For example, I want to disable water that flows from random holes in the mountains, because sometimes it creates massive floods.
These are called “springs” and are a special mapgen feature I have added. This is not editable by a setting, sorry. I could add a setting to disable water and lava springs, but I did not bother to do so yet.
For coders: The mapgen code for springs is in the game mod mcl_mapgen_core.
And replace the inventory with the default minetest inventory.
This is not trivially possible and would require a gameplay change. The default Minetest inventory has 4×8 slots, while MineClone 2 has 4×9 slots. Changing the inventory size is out of question.
Apart from the gameplay change, the inventory needs a complete rewrite for this to work and is definitely not
trivial. The hard part is not actually getting the default inventory back, but also rewriting the creative inventory.
For coders: The mod “mcl_inventory” is the mod that adds the MineClone 2 inventory. If you want to change how the inventory works, you need to look here.
I also need to know how to make the grass behave like in the Mineclone 2 subgame, so that it doesn't take too much hits to destroy it. And in the default minetest game, the tree trunks are dug into the ground 1 block deep, which doesn't seem to happen in this subgame, how do I change that?
Tall grass in MineClone 2 is mined instantly. To make any node being broken instantly by any tool (including hand), add the group dig_immediate = 3
to the node definition. This group is a so-called special group and works in all games. Do not
as other people suggestes, this is wrong as MCL2 does not recognize this groups.