So in pragmatic terms, enabling/disabling "extensions" lets you prevent some unnecessary processing loads during compilation.
Obviously one can do everything in "vanilla" (no-"extensions") Haskell just like one could express everything in raw Lambda Calculus. Syntax sugars as always allow for reducing patterns of verbosity --- those provided by "extensions" tend to be such patterns-of-verbosity that don't always occur in-all-projects-all-the-time, just in enough-projects-much-of-the-time.
Most of the aversion to them seems kneejerk "but my other language had another (or none at all) approach to this" --- never understood the strong opinions about GHC extensions. "Other-language" typically also delights in a culture of repetetively verbose syntax itself and no such APIs to hack new language constructs into the compiler in a plug-and-play manner (without forking).
And yes one can enable these via cabal file or GHC -X flags, but there's something to be said for per-module pragmas: they only activate where needed, and it aids the code reader as to what non-vanilla syntactic constructs are used in the-module-at-hand.