I'm sorry you're no further forward
I expect Tom is quite weak from his weight loss as much as anything. Is he drinking OK - not dehydrated? The vet could give fluids - that always makes a bun feel better.
I don't understand the risk of severe diarrhoea with treatment for Syphilis? It's a penicillin injection, and they are usually incredibly well tolerated in rabbits. An injection by-passes the gut (which is what would cause the issue) and has benefits without the drawbacks ...
A steroid injection, though controversial, might be indicated in Tom's case. It would most likely make him hungry and want to eat, and in addition make him feel better.
You saw a specialist though - these are just my thoughts based on what you've said about Tom.
Still sending vibes x