One thing I haven’t seen mentioned on here is that the Auto Train’s consist is limited by the HEP capacity. The explanation I’ve heard from the inside is that Amtrak wants to add sleeper capacity to increase revenue, but the trade off is either remove a coach car during peak season, which offsets the revenue gains, or remove a coach diner. But with the latter choice, the remaining food service cars then wouldn’t have the capacity to serve a full train. So, you drop the coach meals, save a bunch of costs in the process, and still benefit from the added sleeper revenue.
The other explanation I’ve heard is that Richard Anderson is a three-headed demon-monster that feasts on the souls of sugar plum fairies.