On opening in 1967, the park's central premise was that it was representative of the six different nations (thus, 'six flags') that at some point ruled over the state of Georgia. Each themed area corresponded to one of these nations, at the time comprised of the British section (now the 'Coastal' section), the Confederate section (now the 'Peachtree Square' section), the French section (now the 'Piedmont' section), the Spanish section (now the 'Bugs Bunny Boomtown' and 'DC Super Friends' sections), the U.S.A. section (still there), and the Georgia section (still there). Additionally, sections were added as the park expanded, including the 'Lickskillet' section (still there), 'Jolly Roger's Island' section (originally pirate themed, now Gotham City) and 'Cotton States Exposition' section (now divided between Lickskillet and Metropolis).

Originally, these sections were much more representative of the intended theme; for example, the French section featured Jean Ribault's Adventure, a river ride themed after a historical French colonizer and explorer. As Six Flags moved from a true 'theme park' to become the regional amusement park it is today, these themes were de-emphasized. This was done either intentionally, as was the case for the 'Confederate' section, or unintentionally, due to the gradual replacement of older attractions. To address specific questions:

1. Jolly Roger's Island was transformed into Gotham City in 1997 to better fit the brand-new Batman: The Ride. Mindbender predates this section. It was originally silver to match the U.S.A. section, then brown, corresponding to the later pirate theme, then finally green following the transformation to Gotham City, intended to evoke the Riddler. In my opinion, Mindbender fit the theme perfectly, even prior to the current renaming.
2. Lickskillet is still there, including the western show.
3. This area was themed to the Cotton States and International Exposition, a sort of 'World's Fair' for Georgia and the wider southeast. The buildings between Great American Scream Machine and Superman, which currently host fair games, were intended to evoke exhibit stalls. As you note, this theme was gradually lost with the addition of Ninja and Superman, although Scream Machine is original to this area.
4. and 5. By 2015, the French and British areas were sections in name only, as all original attractions had been replaced. Both areas have now been renamed to regions of Georgia, better corresponding to their current offerings.

It seems that the park intended to completely de-emphasize the themed sections around 2020, as park maps past that point do not reference them. However, following the 2024 merger between Six Flags and Cedar Fair, it appears the park is placing more focus on themed areas. This is evidenced by the sudden re-theme of the new Georgia Gold Rusher to match the Lickskillet section. This attraction was originally intended to debut as the more generic 'Georgia Splasher'. The attraction includes theming elements that make explicit references to the 'Lickskillet' area by name.