Basically, yes.
For example, if you do a multi-city trip where the rail fare (presumably excluding any Acela Express/Metroliner segments) exceeds the "Explore America" fare for the trip you are booking (with respect to time of year traveling, and number of "regions" traveled), the rail fare will be calculated at the appropriate Explore America rate.
If you want to do more than four segments, you'll have to call 1-800-USA-RAIL, which, unfortunately, makes you ineligible for any internet booking discounts, but will save you money if you have a really big itinerary to plan.
Also, it's not really a "pass," even though it is included in the Rail Passes section of the website. It's more of a maximum rail fare you will pay for booking a long reservation, provided you meet the restrictions listed.