I dug back into my Tyco catalog collection to see what the history of the operating hopper car was. Here is what I found:
The car first appeared in the 1961 catalog as a single car. It was a part of almost every freight train consist in that catalog. The first set you saw it in was an Illinois Central "Black Diamond" set with the brand-new GP-20 (also introduced that year) followed by three hopper cars decorated in Burlington, U.S. Navy, and Reading. Here is what the catalog said regarding the individual car:
"Now, for the first time, remote control of Hopper Car unloading, car after car, bin by bin, exactly as you want. Gravity-sealed gate can only be opened by actuator. Gates clear all switches, etc. Operating Hoppers in 5 road names. T330A-Reading, T330B-CB&Q, T330C-Pennsylvania, *T330D-Chesapeake & Ohio, *T330E-US Navy - Each $2.79. Gate Actuator w/9" track section No. 15735, $.75; Gate Actuator only No. 5736, $.49."
Now, I don't understand why the Reading, Burlington, and Pennsy cars were not also designated (by the *) as new cars in that catalog unless they were introduced mid-season. They definitely do not appear in the 1960 catalog because the only hopper car in that catalog was a scale, two-bay non-operating hopper that actually looked pretty nice; very similar to Athearn's ribbed 2-bay hopper. I have never actually seen that particular car, before. But, I think that Mantua might have reproduced it in the 1980's.
Now, as far as the hopper car Unloading Set goes, that didn't appear until the 1962 catalog. It was introduced in a half-page spread on the back cover of that catalog. There was quite a bit of text about it, detailing the trestles, the concave/convex track, coal, etc. It was offered as two options: #862 complete set with the operating car and all track/trestles etc., and the other #861 with just the track, trestles, etc. but no car. The picture showed a Burlington hopper car atop the trestle. However, the text made no mention of road names available with the set. Of all the sets I saw when I was a kid, only the Boston & Maine car was available, but that would have been around 1966-67. In all of the other catalogs I looked at, it was primarily a Virginian car, but a few had the B&M car, instead. In no case did you ever see both.
Also in the 1962 catalog, the single hopper car was made available in the new road names of *T330-F Virginian and *T330-G Boston & Maine. In following years, the C, D, and E road names were dropped.
In 1963, the Sugar Hopper was introduced, which was the same car but with a high-rise cover. It was made available in these road names: T332A-Brach's Candies, T332B-Spreckle's Sugar, and *T332C-Holly Sugar (flagged as the only new car). Again, cars A and B must have been mid-season introductions. In subsequent years, only C was produced.
It wasn't until 1966 that the Cement Hopper was introduced with a top-level cover. It was made available only in the T336-Monon road name. As near as I have been able to determine, no other road names were offered. All of the catalogs had no letter-suffix on the number; just T336.
Again, through the years, as the toy train market seemed to diminish, road names were dropped, often leaving only one road name for the less-popular cars and about half the road names for the others. The covered hoppers disappeared in the early 1970's and the only operating hoppers left were the B&M and the Virginian. And they were available only in train sets and in the unloading hopper accessory set. Eventually, only the Virginian was all that was available; and that only in a set. I bought one in the gold-boxed sets in the late 80's just for the heck of it. It was just exactly like my B&M set I got for Christmas as a kid in 1968 (which was in a blister-pack instead of a box). I was flooded with childhood memories. It was like Christmas 1968 all over again.
I hope that this information has served to answer your questions. It's a fascinating history.