<?php
foreach (['upload_files','upload_images'] as $option){
    if($setting = $modx->getObject('modSystemSetting',['key'=>$option])){
        $extensions = explode(',',$setting->get('value'));
        if(!in_array('webp',$extensions)){
            $extensions[] = 'webp';
            $setting->set('value',implode(',',$extensions));
            $setting->save();
        }
    }
}

$ms2images  = 2;
$source = $modx->getObject('modMediaSource',$ms2images);
$props = $source->get('properties');
$props['thumbnailType']['options'][] = ['text'=>'webp','value'=>'webp'];
$props['imageExtensions']['value'] .= ',webp';
$props['allowedFileTypes']['value'] .= ',webp';
$source->set('properties',$props);
$source->save();