The term "prototype", in its literal sense, is a bit of a misnomer when it comes to these books. I've heard it argued that a better term would probably be "precursor". With the exception of the "Man in the Ant-hill" story in TTA 27, there are no direct literal connections to the "prototypes" and the actual Marvel characters that they are associated with.
However, I do think its important to the comic book historian to be able to link these pre-hero "precursors" to the later Marvel characters that would draw inspiration from them. These stories are a great insight to the early days of Marvel.
I have always been a fan of the very early Silver Age Marvel stories and just when I thought I had read all of them, I discovered that there were earlier stories that were drawn by the same artists and written in the same style. When I sought these books out, I realized that there were more to these stories than just fantasy tales - they were a springboard of ideas that would be recycled and refined into some of Marvels most popular characters.
Prototypes are fun to read and even more fun to find. There are prototypes to be found beyond the pre-hero books, my children...look for them in DC, Charlton, & Harvey fantasy titles (to name a few).
Bill