The website always applied penalties, IIRC, you had to call to get the waivers. At least that was the way it was when the waivers were first introduced. Try calling to cancel if you haven't already executed the transaction. Can't say if they'll be able to reverse it if you did, probably what's done is done.
And yes, it does sound right, without the waivers, there is a stiffish penalty for cancelling sleepers at 120 days or less out. Which goes up again at 14 days.
Many agents were applying the modification waivers to cancellations, I was able to do that myself last year with AGR points and an AGR agent, but I heard some weren't, or the policy changed. It's Amtrak, so inconsistency would be no surprise. In any case, you probably have to process the cancellation through an agent to have any chance of getting the fees waived.
Another possibility is to modify to a "holding" itinerary some months out, then modify that once you are able to make other actual plans. No limit on mods that I am aware of, have done up to three (original and two mods) myself. Note it doesn't have to be the same endpoints, it can be anything as long as its Amtrak.
