I was at Topper a year ago, and the article in the OP is misleading. The stratigraphy of Topper is roughly like so:
An upper layer of mostly debittage (fragments from the knapping process) and latter, historical points.
A second layer immediatly under that of middle and late paleo debris and an occassional tool.
Then, after slowly removing nearly 18 inches of earth, in which there is nothing, do we reach the clovis layer. Again, it is mostly debris from knapping and breakage, but Clovis tools are also found, especially handaxes.
Beneath that, at various depths in the Topper site, we find pre-Clovis artifacts. On the pleistocene terrace pit, down by the Savannah river, there are artifacts dated at 50,000+ yrs. old.
Throughout the complex, there is evidence of old firepits and hearths. The hearths were for thermal heating the chert, which makes it stronger. These show up as thick charcoal deposits. There is NOT a "black mat" at Topper like some other sites have that are associated with the Comet theory.
If there are any other questions, I'll try to answer 'em.