Wow, I haven't heard the term "Nun's Knickers" in something like 20 years. Blast from the past.
They generally are not needed, and yes, will affect a followfocus unit if you let them get caught in the gearing... which is very easy to do. I haven't used them with a matte box, but our teleprompter has a similar cloth surround that gets caught in the gearing very easily if I'm not careful.
Most pro matte boxes will come with a set of rubber "donut" masks that fit at the rear of the matte box, in different sizes appropriate for the lenses. You don't have to have a light-tight fit there. All my lenses except one have a standard cine 80mm front, and the donut I use has about a quarter-inch space all around the lens and it works fine. The only way that would ever be an issue is if you had hard direct sunlight straight behind you reflecting off a filter and then back into the lens. Since I almost always use my matte box naked (no filters), it's not an issue.
I can highly recommend the swing-away matte box from RedrockMicro. It's super well made and a fraction of the cost of something like an Arri swing-away box. Or if you are really on a budget, Cavision makes some decent lower-end non-swing-away boxes that are ultra cheap (few hundred).
T2
__________________________________
Todd Terry
Creative Director
Fantastic Plastic Entertainment, Inc.
fantasticplastic.com