The key difference here lies in when in gameplay the player would choose the roleplaying scenario. For all the other, existing suggested "reasons" for your fort, you start with a normal worldgen, pick a normal civ, pick a reason for your fort, and choose your site (certain reasons for the fort may pick the site for you--for instance, a trading hub would have to be situated at a major crossroads, not out in the middle of nowhere). You may also choose to embark with no real "reason" for the fort at all, just like the game is now.
For the game to generate a "Holdout" fort, however, you would need to pick that theme before worldgen even started. That would force a worldgen with different enemy-behavior parameters, so that goblins & other beasties would attack, but never actually destroy, the last settlement of any civilization until the entire world is pretty much covered in Evil biomes. Once there's only one dwarf civ left, the beasties whittle its population down to just a handful, and then leave--and that's where worldgen stops, you can't set the ending year, and the only possible embark location is essentially a Reclaim of the existing "last stronghold". Now, there's nothing wrong with arranging a setup like this (here's where NW_Kohaku & I disagree), it's just very different from how the game is currently arranged, as well as the direction in which the game is currently moving. Now, Dwarf Fortress may one day come to encompass this sort of "flavored" worldgen, but that day won't be coming for many years yet. For now, you'd be far better off tweaking your own worldgens to find/create just such a scenario for yourself, and posting the savegame for others to use, and/or asking other Holdout aficionados to do the same thing.