It's a case by case thing. If a Sythe rule trumps a TOS, then I guess it's rendered useless.
In cases where you're seeking reimbursement, for example, it can be to your advantage. If you were promised X, Y and Z but the user fell short of the Z condition; you'd be entitled to amendments, re-completion of service or a refund (whether full or partial) to have your product completed to X, Y and Z standard that was promised.
TOS' clauses like "pay for firecape, if I fail the cape, you don't get refunded" etc would all be trumped by Sythe rules in most cases. I would personally handle it that way, anyway. It's very much case-by-case and unless there is an outlined situation then it's hard to say what the outcome would be.