Since you mentioned ferrules, I'm assuming it has through-body stringing rather than a tailpiece?
In that case, the string angle behind the bridge will be even steeper than it would be with a standard tailpiece (unless the ferrules are set a really long way back from the bridge). So it's very likely that some of the strings are going to come into contact with the back of the bridge and there's not much you can do about it.
The only ways I can think to avoid it are:
1. A very low bridge with very tall saddles (good luck with that! :P )
2. A narrower bridge, like a Gibson ABR-1 - and even that might have the same problem if you currently have the issue with both the E and B, it's usually just the high E.
Having said all that, I know people always make a fuss about this issue, and it does seem "wrong" that the string tension should be "interrupted" at two points rather than just one, but I've never seen it demonstrated that it really does have an adverse effect on tone.