Important and complex subject...
1. The help for Shared Teams says something to the effect that you have to have Shared Teams in place before creating a Product or Library that will use them. Which a) eliminates their use for anyone already using the system in production b) seems like it forces you to have all Shared Teams thought thru for all time before creating any Product or Library. Because of this, we have (so far at least) ignore Shared Teams.
2. OTB, very few ACL's are at Site or Org level. The vast majority are created at Product / Library level because they are included in the Product and Library templates. It creates an absolute maintenance / troubleshooting nightmare to have them spread out this way, and we fully agree that it's best to put all that are common one level up (at Org level). Essential to make this work is to create your own Product and Library templates with minimal ACL's in them so that all future contexts inherit from Org level.
3. Be careful about applying the same permissions everywhere. At a minimum, you probably need at least one restricted-access Library for things like Drawing Formats. Also, purchased standard parts (screws, nuts, etc.) which are used pretty much everywhere need a different process from custom items and generally need different access controls.
4. One major irritation is that at Site or Org level, you cannot see what ACL's are in each Product / Library - you have to go to each in order to examine. OTB but hidden pretty deep is a report that lists all ACL's, but it's highly unreadable. We created a query builder report that dumps to Excel for this purpose - far more usable.
5. Careful about putting things at the Org /Default domain also. If you ever install ProjectLink in the future, they will also then affect Projects. Best to go one level down to Org/PDM/Default.
6. Also, plan Teams carefully (fortunately all but Shared Teams are very editable). Much more flexible to use Team Templates in general than Context Teams.
Big, complex and difficult subject. All of this we learned gradually the hard way - could really use better and more realistic examples in this area from PTC in the business admin guide and PTC U, etc.