I used the Harley SE hi flow air filter on my Rushmore SG and it is substantially bigger than the stock unit which itself was much better than the previous units.
The SE units come with a new mounting bracket which replaces the breather with an internal design built into the new bracket. After you replace the bracket the new filter gets installed and the factory air cover goes back on (less the plastic back shroud). The Kit comes with a replacement plate that says Screamin' Eagle which replaces the factory "103" plate....the plates are both held on with a velcro strip and you have to remove this to take the factory cover off anyhow.
Hope this helps explain the breather tube issue....................BTW I found the SE unit to be very well made and at ~$110 discounted online it was a well engineered solution for me trying to keep the factory look.