With regard to using chains in lieu of butt bars, I have used two techniques for protection. I believe that either a chain or a bar provides extra security on the off chance that a door comes open when travelling and it also prevents a horse from rushing back as soon as the back door is open.
In the straight load, I slid agricultural hose over the chains and then put on the clips/snaps (one side has a panic snap on it). The hose is black in colour, sturdy and stiff but with some flexion - it acts like a safety shield and consequently there is nothing to scrape the horses. It can be purchased from any agricultural store that deals in hydraulic equipment, etc., or chances are (if you're on a farm) there are clean scrap pieces left over from other projects.
In the slant load, I used pipe insulation and my favourite tool - duct tape plus regular clip on one end and panic snap on the other. Pipe insulation is dark grey in colour, is made from thick foam type material (it's meant to insulate water pipes in houses, etc., to prevent freezing) and much more flexible than the hose. I used that for this one as the chain is a lot longer and it's easier to manage. You need to do a wrap of duct tape at the ends and a couple of places in the centre as the insulation has a seam in it (so it can wrap around a connected pipe) and it would come off otherwise. Once it's taped up, it provides good scrape protection from the chain.