Attached patch adds a setting RTE.default.proc.preserveExternalURLs, which if set to 1 fixes this issue. If someone needs the URLs to be relative, it can be set to 0.
Index: t3lib/class.t3lib_parsehtml_proc.php =================================================================== --- t3lib/class.t3lib_parsehtml_proc.php +++ t3lib/class.t3lib_parsehtml_proc.php @@ -1549,7 +1549,9 @@ $uP=parse_url($info['relUrl']); if (!strcmp('#'.$siteUrl_parts['fragment'],$info['relUrl'])) { - $info['url']=$info['relUrl']; + if ($this->tsConfig['proc.']['preserveExternalURLs'] != 1) { + $info['url']=$info['relUrl']; + } $info['type']='anchor'; } elseif (!trim($uP['path']) || !strcmp($uP['path'],'index.php')) { $pp = explode('id=',$uP['query']); @@ -1563,7 +1565,9 @@ $info['query'] = $parameters[0]?'&'.implode('&', $parameters):''; } } else { - $info['url']=$info['relUrl']; + if ($this->tsConfig['proc.']['preserveExternalURLs'] != 1) { + $info['url']=$info['relUrl']; + } $info['type']='file'; } } else { Index: typo3/sysext/rtehtmlarea/res/proc/pageTSConfig.txt =================================================================== --- typo3/sysext/rtehtmlarea/res/proc/pageTSConfig.txt +++ typo3/sysext/rtehtmlarea/res/proc/pageTSConfig.txt @@ -145,6 +145,9 @@ ## AVOID CONTENT BEING HSC'ed TWICE htmlSpecialChars = 0 } + + ## Leave external URLs as set. If set to 0, local URLs will be transformed to relative paths. + preserveExternalURLs = 1 } ## Use same RTE processing rules in FE