I don't know for sure, but I do know this:
* the 'masq' template fragments step through all keys named 'service' when looking for 'TCPPort', 'UDPPort', 'Allowhosts' and 'Denyhosts'.
* the ibay template fragments look for and process all 'ibay' keys
* the user directory template fragments look for and process all 'user' keys
I suspect that all pseudonym keys are processed when creating the various qmail and qpsmtpd config files.
I think local networks are identified and processed using a 'key'.
From this I assume that the general purpose of the keys is to allow common processing of similar items in the SME templating system.
Creating your own keys should not cause any problems (said the know-nothing non-programmer), but proper key selection will optimize the integration of your modifications with SME.
There are now several contribs that create their own entire databases (affa and webshare, to name two)