RSyntaxTextArea.markAll() is much slower than marking stuff via MarkOccurrencesSupport, and there's no real reason for this. Note it's typically only a problem in the pedantic worst-case (many thousands of instances of the token to "mark"), but it is still something that should be rectified.
This is fixed in the latest GitHub commit. "Mark All" is much faster now than it was previously, on par with "Mark Occurrences". This will be in the upcoming 2.5.1 release.