6 year courses are basically the same as 5 year courses but intercalating is mandatory: 100% of people take the intercalated BSc. Basically, you get an extra few points out of 100 when applying for foundation year posts. The intercalated degree from the 6 year course is no better than that done during a 5 year course (thus turning the 5 year course into a 6 year course), it is purely down to the fact that for most 5-year courses it is not mandatory to do an intercalated degree if you don't want to.
The only positive I can think of is that for most 5-year courses, you generally need to be in the top x% of the year to intercalate. If you're not you miss out on the chance, while everybody on the 6-year course does intercalate.