If you need absolute urls for a specific extension, like a newsletter or email extension, then it is generally a good idea to create a new editor profile specifically for this extension, and then set the Relative URLs option to No for this profile only.

To do this:

1. Go to Components -> JCE Editor Profiles.
2. Select the "Default" profile, or your main profile, and click the Copy button.
3. Click on the name of the new profile to edit it, then in the Setup tab, give the profile a new Name and Description, set Enabled to Yes, and set the Ordering to Order First.
   
4. In the Assignment section, set Components to Select from List and then select the component to assign the profile to, eg: AcyMailing.
   
5. Click on the Editor Profiles tab, then set the Relative URLs option to No.
   
6. Set any other profiles options as required, then click the Save button.

Now, when you create or editi an item in your mailing/newsletter extension, you will be using this new profile, with all URLs set to absolute.

JCE always inserts links using the raw form, eg: https://myspectacularsite.com/administrator/index.php?option=com_content&view=article&layout=edit&id=242

The Joomla SEF plugin processes these links when the content is displayed in the front-end, converting the raw url into a SEF url.

I am of the opinion that the newsletter / mailing extension should be doing both the absolute URL conversion and SEF URL processing itself, when the email is sent, but none of them do, hence the need for the workaround I posted above.

I have added an option in JCE Pro 2.8.1 to convert the links to SEF urls too. You can set this option in Editor Profiles -> Plugin Parameters -> Link



You can download JCE Pro 2.8.1 Beta 1 for testing here - https://www.joomlacontenteditor.net/downloads/editor/pro/development