TYPO3 Core

I fixed it with adding this in registerRTEinJS() in Typo3 4.7:

if( $GLOBALS['TSFE']->config['config']['absRefPrefix'] && !$GLOBALS['TSFE']->config['config']['baseURL'] &&
    t3lib_extMgm::isLoaded( 'realurl' ) )
{    
    $baseURL = $GLOBALS['TSFE']->config['config']['absRefPrefix'];
    if( !preg_match( '@^https?://@i', $baseURL ) )
    {
        if( strpos( $baseURL, '/' ) === 0 )
        {
            $baseURL = substr( $baseURL, 1 );
        }
        $baseURL = t3lib_div::getIndpEnv( 'TYPO3_SITE_URL' ) . $baseURL;
    }
    $configureRTEInJavascriptString .= '
        RTEarea[editornumber].baseURL = "' . $baseURL . '";';
}

A solution could be adding the code in getRteInitJsCode():

$baseURLConfig = '';
if( $GLOBALS['TSFE']->config['config']['absRefPrefix'] && !$GLOBALS['TSFE']->config['config']['baseURL'] &&
    t3lib_extMgm::isLoaded( 'realurl' ) )
{    
    $baseURL = $GLOBALS['TSFE']->config['config']['absRefPrefix'];
    if( !preg_match( '@^https?://@i', $baseURL ) )
    {
        if( strpos( $baseURL, '/' ) === 0 )
        {
            $baseURL = substr( $baseURL, 1 );
        }
        $baseURL = t3lib_div::getIndpEnv( 'TYPO3_SITE_URL' ) . $baseURL;
    }
    $baseURLConfig .= '
        RTEarea[0].baseURL = "' . $baseURL . '";';
}

return '
    if (typeof(RTEarea) == "undefined") {
        RTEarea = new Object();
        RTEarea[0] = new Object();' .
        $baseURLConfig . '
...

And using the current JavaScript method only if baseURL is not set:

HTMLArea.Config = function (editorId) {
...
    this.baseURL = HTMLArea.baseURL;
    if( !this.baseURL )
    {
            // BaseURL to be included in the iframe document
        this.baseURL = document.baseURI;
    }
...

Because the absRefPrefix is automatically prepanded to the CSS pathes on page rendering it is applied twice with this solution. So I modified the code as follows:

if( $GLOBALS['TSFE']->config['config']['absRefPrefix'] && !$GLOBALS['TSFE']->config['config']['baseURL'] && 
    t3lib_extMgm::isLoaded( 'realurl' ) )
{
    $baseURL = $GLOBALS['TSFE']->config['config']['absRefPrefix'];
    if( !preg_match( '@^https?://@i', $baseURL ) )
    {
        if( strpos( $baseURL, '/' ) === 0 )
        {
            $baseURL = t3lib_div::getIndpEnv( 'TYPO3_REQUEST_HOST' );
        }
        else
        {
            $baseURL = t3lib_div::getIndpEnv( 'TYPO3_SITE_URL' );
        }                        
    }
...

Could you please try if this patch could fix your issue:
https://review.typo3.org/#/c/37799/