Hennessey's 6th gens use the stock box with a drop in filter all the way up to the HPE 650 NA and HPE 750 supercharged. After that they use a procharger which isn't compatible with the stock box. Their 5th gen packages all replaced the stock box. They probably found through their testing the stock box with drop in flows the best in the 6th gen.
HPE 650
http://www.hennesseyperformance.com/...pe650-upgrade/
HPE 750
http://www.hennesseyperformance.com/...arged-upgrade/
5th Gen HPE 550
http://www.hennesseyperformance.com/...pe550-upgrade/