When I said pattern, I was pointing to some recent devs I've been involved in, in which there existed a global syspref, and we added category-spcific overrides (for example password strength enforcement) or if an itemtype is excluded from LocalHoldsPriority.
In those cases we added a new column to the related table (categories, itemtypes).
As a general rule, I'd say most of the sysprefs could be moved as 'global' (i.e. no library, on item type or category) unless there's room to enhance them to make them per some of the other criterias.
I personally prefer to keep my dev as-is (it is almost finished and happy with the smtp_servers table). But there was some room for thinking about a more general approach to sysprefs. which sometimes are combined with information from other places and it is not that easy for the end user to understand the different interactions between them. Take the password strength sysprefs, and the category-specific overrides. It would be better to provide a nice UI for setting global and on a per-category basis this. And we could have some flag to identify the ones to be displayed on the system preferences pages specifically.
Regarding 'how to choose the right SMTP' server, I think it really depends on the context. My guess is we should use the library from which the 'From' attribute is picked. And we will be safe.