I swear by barrier cream too. Lather it on up to the knees/hocks. The one I used had a yellow and black label, darned if I can remember the name just now but it really did the job! Used to scrub with warm water and antibacterial shampoo first, towel the worst off and let dry completely, ideally in somewhere clean and dry, or if need be "hack and go"! Then lather up with cream once dry. Seriously, I used loads of the stuff.
I did this once a week, as the barrier cream stayed on unless shampooed out. The rest of the time it was a quick rinse off with the hose if wet and muddy, or a good brush if dry. Cleared my mare up in under a month, but she only had a mild case to begin with thankfully.
What we've really got is an infection which has got into the area weakened by mud fever.......but as you say it's a cover all explanation. Still a bugger whatever you call it. I believe the technical term is pastern dermatitis.
When I had to call the vet out recently for bad mud fever he said mud fever is just a general term for scabby legs, which can have a lot of different causes. I guess therefore there is no one size fits all treatment. That said, he did give me antibiotic cream, which did clear it up.
I am dealing with a horrid case of this - almost 4 weeks worth so far.... So far dhorse has had 5 penicillin jabs (his leg swelled up hugely and you could see the infection travelling up his leg at one point), the keep it covered and soft treatment, and now after a week of cream and spray and being uncovered we've finally reached the stage where it has scabbed properly and hopefully it won't be long before it goes. I'm not holding my breath though as it keeps erupting in new places - the original bit is well healed, we're now on eruption number 4.
I've never had to deal with it before and can't believe how persistent the infection is. He's even had little bald patches up on his neck and hind quarters which are related to the infection - he's not looking his best poor boy!
There are so many different thoughts on how to treat it, it's mostly a case of trial and error once it gets hold - the vet has been tearing his hair out with it, and been very helpful (I've been sending photo updates every other day, and he's been "visiting in passing" free regularly, bless him.
I think it's because the skin needs to stay dry to heal coz mud fever is essentially caused by the skin becoming too wet which allows the bacteria to take hold so by softening the skin with cream can make it worse.