I don't know about Mako templates, but for Bottle SimpleTemplates you can use BaseTemplate.default:
bottle.BaseTemplate.defaults['session'] = bottle.request.environ.get('beaker.session')
However, since you are setting that at application instantiation time, bottle.request may not be valid. So you may need to turn it into something that does lazy evaluation when the value is requested.
Perhaps BaseTemplate.defaults gets fed into the Mako templates, or maybe Mako provides a similar mechanism for setting the defaults?
I hope this helps point you in the right direction.