So on a wimp I did your change, and yes, it makes it unreasonable to dig down past stone. But guess what, flagstone blocks also have the stone property, so now it is very easy to have an impregnable above ground base. So I guess I need to mod out flagstone next?
Well, this is an issue. It is unfortunate that the developers are not on the ball here and fixing this. It's not like I'm being paid to figure out how to fix the balance of their game.
I think the solution is to reset the stone material back to 500. Instead, in the blocks.xml file we can go to block id 1 "stone" and change the material value to MrConcrete. This will still increase the strength of bedrock (in this case, I use bedrock to refer to actual geologic bedrock) twelve fold. Indeed, drilling into bedrock can often be much more difficult than mere concrete, so its important to have impenetrable rock just a few meters below the surface of the ground.
Furthermore, to discourage any stubborn miners, we can also edit the resources dropped. It's not clear, because the developers didn't comment their file, but it looks like maybe we can just delete the lines which grant iron fragments. We should also do this for all the above ground boulders. We can find them in block id 630, where we simply delete iron, coal, lead, and potassium from the drops.
Someone else mentioned the exploit of producing this new bedrock, so we will go into the recipes.xml and I believe we can change recipe name="stone" by increasing the resource cost a hundred fold. So you can produce it, but it is very difficult to do.
The nice thing about these adjustments is that there remain iron deposits below ground, but you have to drill into the bedrock to get it, and you can't just get free iron by bashing at granite.
Of course, in the desert we need to also address the underground dwellers. A simple fix is to edit materials.xml entry for Msandstone, and change the maxdamage value to 1000. We will also adjust the stability glue value to 9, making sandstone behave more like actual sand, which should keep falling as you dig.
We also need bigger biomes, so in rwgmixer.xml I'm going to change cell_size to 18000, and hopefully that makes each biome ten times larger.