Beyond funding in general, I'd be very interested in hearing how any single-payer system intends to handle reimbursement negotiations with hospitals. If you retain for-profit hospitals, there's going to be a conflict of interest between the hospital wanting maximum reimbursement and the government wanting to minimise it.
How does the bill intend to prevent for-profit hospitals from basically scalping the government, and causing costs to explode out of control? They can't do that in in a multi-payer system because insurers might exclude them from the coverage (or simply force the patient to pay) But if the government uses the same tact, that would instantly bankrupt the hospital, which I doubt is something anyone wants. Will there be government administrators determining what parts of a bill are justified, and which are not? By which criteria? How much are hospital staff allowed to earn? How deep is the micro-management intended to go, and is that actually what people want?
In a sense, going all-out on single-payer and nationalising all hospitals and clinics would be easier. That way, the government could manage all parts of the system and eliminate conflicts of interest. Bernie's proposed hybrid system would be much more complex, and have that many more potential pitfalls.
And that's how it worked in his original plan. Except people misconstrued it and characterized the additional payroll tax as a tax coming directly out of the employee's check.
That's mostly semantics. Payroll taxes are still indirectly payed by the employee because the employer will simply end up taking it out of their potential pay, one way or the other. Either that, or hire fewer workers, or raise prices on produced goods. All costs filter down.