Mine is connected to the primary airbox (standard), but I seem to be getting water in the oil as I get the Mayo problem as discussed here - http://www.triumphrat.net/hinckley-classic-triples/233419-water-in-the-oil-emulsified-mayo.html.Arferbrick: My vent line was attached to the primary airbox until I switched to pods. Not sure what circumstances would lead one to connect it to the secondary air box...
In order to stop it, or at least minimise the water ingress I want to add a filter to the end of the breather pipe, but I don't think putting a small filter inside the primary airbox would be a very good idea as it would (I'm sure) disrupt the airflow to the carbs.
As modifying the breather is illegal here, the only other option I can see is to re-route the breather to the rear airbox where airflow isn't an issue, and only a very keen eye would notice the modification.
I can then filter the air that gets sucked back into the breather, hopefully keeping some moisture out, while still allowing any exhausted gasses (and/or spat out oil) to be sent through the engine for burning.