Without looking at the code (which I should probably do but you could to :) master templates have always gone in the www tree and I've always assumed that's an artifact of the implementation of the master tag in acs-templating.
I'd prefer it go into /templates (but aren't we using /lib?) ...
BTW I'm currently working on the portal system - have it running under subsites without .LRN actually - and all the .LRN portlets store their templates in /www, which is bad. They should certainly be elsewhere (/templates or /lib whichever is right) rather than available through the http: protocol because they're meant to be included ...
