Seeing that no one has answered your question, and having a little time here over lunch, I'll give you my impressions.
Focus on Freight Cars is simply a collection of volumes of freight car photos that were in a collection that Ted was given access to. Although the collection of negatives belonged to a man named Michael Urac, I don't believe he was the photographer. The photos were all taken in Southern California, the Los Angeles area, IIRC, in the mid to late 1930s. At any rate, the photos are all clear, well exposed shots showing to good advantage the details of the cars. There is no discernible rhyme or reason for what got photographed, but as I understand the photographer took the pictures with the intent of building models. So they are very much the type of photos I wish I could go trackside today and obtain. Most of the cars are clean, no doubt to show the lettering to good advantage. Although the paint schemes have sometimes changed by my modeling era, oftentimes the details of the cars have not, so I find these books very useful.
In contradistinction, the Reference Manuals are much more comprehensive in scope, although they are not exhaustive in their coverage. The boxcar and tank car volumes cover the most numerous types of cars for the largest railroads in the US and Canada. These volumes provide an economical and comprehensive overview of the freight car types they cover, for a good portion of the steam era. They are excellent reference sources.
The paper quality and photo reproduction is much better in the FOFC series, however the photos in the Reference Manuals are perfectly usable for modeling. The Reference manuals are much thicker volumes, and would cost much more if printed to the standards of the FOFC books.
The volumes are complementary in my opinion. I buy both series as they become available, and many on this list do the same.