I don't know if I can make this any clearer for you or not. In the old days of Europe on $5/$10/$50 a day (depending on the year) the rail pass was a no-brainer good deal. But now at $500 a day with computers and internet it is a very different travel situation. At the one time most of the trains were the same. Just a matter of how many stops made along the way. Easy to do, get on, get off, and the train pass was the way to go. That myth stills exists today.
With the advent of high speed trains, computers, on-line purchases, etc., most of the rail systems have gone to tiered pricing structure where early purchases on-line are offered at discount, sometimes deep discounts but, like our airlines, those tickets come with restrictions and limitations such as no change, no refund. The discounts on advance sales really undermine the value of a rail pass IF you are willing to commit to a fixed schedule. The rail pass still provides a lot of flexibility but you now pay for that flexibility. And now with the convenience of high speed trains, you pay a premium for using the fast trains.
Each rail system (country) determines how they will treat rail passes. I think it is safe to say that all systems charge an extra fee for a seat reservation - can be expensive. France is notorious for the limiting the passes accepted per train and for charging high seat reservations fees that sometimes are more expensive than a discounted ticket. Germany has a mix of reserved seats so a pass work much easier in Germany. Italy requires a seat reservation for all trains except the Regionale or slowest train. The surcharge in Italy is very reasonable from 8 to 10 euro per leg depending on the train.
Since the train pass is not automatically a good deal, you need to do the homework. Determine you schedule, price it out on each train site, throw in 10 to 15 for a reservation for each leg, and will show if you save money with a pass. A quick way to look at a rail pass value is to divided the days of train travel into the price of the pass. For example - if the pass is $1000 and you are doing 10 days of travel that is $100/day. Then price each day with point to point tickets. That is the only way you know for sure. Conventional wisdom these days is that it is difficult to make a rail pass cost effective if you are willing to take advantage of the discount pricing for on-line purchases. You have to do the homework. The travel agent probably was correct. Just a miss understanding of terms. But if you want a guaranteed seat then you will always have to pay an extra fee for that seat reservation.