I've never really played any mmo's so I'm not really sure how it works for instanced dungeons and areas in other games but I would be surprised if you didn't stand at the front of your house/apartment and press right on the d-pad to get in. Then you'll be able to invite people in once you're inside and if they accept the invite they'll just warp into your safehouse from wherever they are on the map.
I'd think it would possibly be the same for the big garages and you'll probably be able to warp into them from your safehouse also. Although I'm not really sure how people would be able to break in and attack your cars and stuff. Anyone have any insight, I'm really interested to see how it's all going to work.