am I missing something, because it seems to be more than just a matter of scaling from SR3 to SR4

It lets you define your lifestyle in a little more detail. You assign points to 6 categories that determine what your lifestyle is like, and the total number of points determines the cost. So you can have a decent apartment in a bad neighborhood (something between middle and low) and pay a price betwen middle and low for it. Plus, there were edges and flaws available for your home to further customize, so your safehouse could have a nice defensive setup and a secret escape hatch (for an extra cost) or your cheap home might overlook a wall and sewage treatment plant (for a price break).

Cool. Not necessary IMO but it can inspire. Personally I think you can do all that you said without needing rules for it.

Example: Your player wants to live in an abandoned secret undergrown ares tech compund, with no longer electricity, running water or heating. However the complex is fairly large with several rooms and tunnels, well protected at it is undergrown and made of concrete, and the doors (with still operative maglocks) is well camoflagued in the Redmond sewers. The runner is still poor, and can only afford nutrisoy with a few flavors, and his home is otherwise devoid of fuctioning entertainment systems, food processors and other medium-lifestyle utilities.

Although this is basically squatting, I would have the player pay at least low lifestyle, possibly medium if he needed payoffs to the local gangs and bribes to keep any mole-people away. Although if there was something to keep the facility from ever being reused as original (weapons testing) I might keep it at low.

How many points would you use for your system, and what would be the equivalent lifestyle?

It's not exactly my system and I don't have the sprawl survival guide with me at the moment, but I'd eyeball it at:
Area 1 - The area was probably cleared when the complex was built, but it's the Redmond sewers and stuff's probably moving back in
Comforts 1 or 2 - You can steal power, water, etc from somewhere, backups for the maglocks, etc.
Entertainment 0 - As specified, not even a walkman...
Furnishings 0 or 1 - Scavengers haven't taken all the office furniture
Security 4 or 5 - As specified, the basic security still functions
Space 4 or 5 - It was a big complex.

Clocks in at 10-14 points, so right around Low lifestyle. There's probably some edges and flaws that need to be added. Defensive setup, some privacy bonuses, a bunch of negative views, demanding landlord (in this case, the "landlord" is the bribes paid to various groups to stay away), unreliable utilities, maybe a background count. I'd guess it'd end up costing 2000-3000 with all the mods, according to the chart above.