How can you keep saying this? If you turn off migrants or caravans, your game would get harder. Turning things off shouldn't always make your game easier, it should do whatever turning off whatever you turned off does.
I think what the logic here is as follows.
Generally in a game, as you move up the difficulty curve, more features are added. It also plays partially into the learning curve, but for example: in alot of RTS the initial levels may only have infantry and that's all you are fighting. Then as the game gets harder, tanks get thrown in.
So someone playing a hard game is going to want all the features in. If the only way to make the game hard is to turn everything off, its not going to be very interesting. It would be sad if you had to choose between an easy game with alot of fun things to do, or a challenging game where you don't have migrants, or other things that can be fun.
Granted, in some cases it can be absence that increases the difficulty. We discussed risk and reward, and how there would be some risk with using rivers (river raids). However, not having any water at all (in a desert) will have difficulties as well without any direct rewards. Perhaps the desert is its own reward because of mineral deposits. However, the desert is essentially harder because of a lack of a feature (water).
Ultimately I agree that init options should not be in to make the game harder or easier. They should be there to simply toggle whatever they toggle. Some things may happen to make the game harder, some may happen to make the game easier. Some of them just add in risk/rewards.
For example, turning off the sieges gets rid of the risk of attack. But it also gets rid of the reward of getting iron loot from the goblin attackers.
A pop cap helps you avoid difficulties of managing large forts (and can help FPS but that's a different matter), but at the same time it means you have less dwarfs to work on your projects.
Some future init options may make the game easier when turned off, but get rid of features. Some may make the game harder when turned off, but make the game easier. Some may just represent trade offs. There is nothing wrong with this.
Ultimately I don't like the idea of init options killing features. I think it would be better if there were ways in game to avoid the features. Players that don't want sieges could avoid goblin infested areas, or perhaps send tribute to the goblins to sate their greed. Players that don't want migrants could tell their mayor to turn migrants away. Don't want the economy. Maybe your military could enforce the strange communal system your dwarfs use. Or perhaps a liaison could be sent to the king, with a bribe, to hold off the tax collector. Certain things like weather, temp, and pop caps, that relate strongly to FPS, I have no guff with.
I think integrating alot of the init options, or "potential init options," would help keep the game world consistent, and maintain the games integrity as a simulator (Many simulations that allow you to turn off things makes a distinction between simulator mode and "arcade" mode). however, I have nothing against init options or people who want/use them. I just think in some cases they aren't necessary, and integrating the options into the game could add fun new aspects.