1. The distance for noise is only the distance required for you to connect to a part of the matrix that you need access to for whatever action you need to do. So making a call to order a pizza, that's "local" public access so as long as your in a metropolitan area with matrix access your distance is zero. Making a call from Seattle to Tokyo then your need to bounce from Seattle local to Tokyo local ... your going to have a noise issue. Need to hack the Host on the other side town, that does not have local access so you have noise due to distance. What this means in general is that typical everyday matrix use doesn't have to deal with noise issues unless you're out in the boonies, but hacking specific targets means you need to get closer to your target for maximum efficiency.
My headcanon here:
1) there are three kinds of host: Foundation hosts, Cloud hosts, and Local hosts
2) Foundation and Cloud hosts are "global" and appear to float in the sky in the Matrix
2a) Foundation hosts are weird and mysterious, as per canon, but also rare
2b) Cloud hosts are like modern day websites - comprised of a large number of geographically distributed computers linked via very fast, private connections
2c) Mechanically, Cloud and Foundation hosts are the same, although I think maybe there's Host Rating range differences (say Cloud are 3-8 and Foundation are 7-12 or something like that)
3) Local hosts appear at a specific geographic point on the Grid
3a) They are down at "street" level in the Matrix and appear at a fixed point analogous to their real-world location
3b) These are building control systems, security systems, etc - most of the stuff Shadowrunners want to break in to
3c) They have Host ratings of 1-8 or so
4) Users usually take no noise penalty when connecting to or doing stuff within Foundation or Cloud hosts
4a) The Cloud host's nearest node is assumed to be close enough to the user to not see noise
4b) Users might see noise on this link if they're out in the sticks or being jammed, however
4c) Noise here represents your commlink's inability to connect to
anything, not just the host
4d) This noise does not go away once you get inside the host
5) Users take distance-based noise penalties when connecting to Local hosts or other Matrix devices that are not hosts
5a) Noise here represents lag and unreliability due to peer-to-peer routing over distances
5b) This Noise persists even inside the Local host, it doesn't go away once you "get in"
6) Most everyday Matrix stuff - voice/vid calls, social networks, messaging - is done through a Cloud host. You can call Tokyo with no noise penalty because you're doing it through a host, although your device doesn't do anything to show you that's happening unless you do it in VR.
6a) Illegal stuff can't be routed through Cloud hosts; their firewalls are good at detecting and blocking it
7) A small amount of legal, everyday stuff is nearby peer-to-peer: streaming music to your cyberears.
7a) There's rarely any noise penalty here because the range is rarely far enough to matter

Players might run acquire and run Local hosts for their own stuff, but running Cloud hosts is typically beyond their resources
Edit - fixing numerous typos