I think that logic bears repeating:
1) Modern humans could not have made the ca. 800,000-year-old Mata Menge tools.
2) The Mata Menge tools look similar to the Liang Bua tools.
3) H. floresiensis is at Liang Bua.
4) Therefore, H. floresiensis or its ancestors must have made both the Mata Menge tools and the Liang Bua tools.
. . .
The key question beneath the conclusion of the paper is whether item 2 is accurate -- are the Mata Menge tools really similar to the Liang Bua tools? This is where the paper seems weakest to me. It is really a stretch to claim that these assemblages were linked by any kind of tradition.
Many of the traits supposedly common to both assemblages look pretty general to me, too. And Hawks' point that these similarities would imply a common "tradition" lasting 700k years is also well-taken.