I'm also having this issue in 5.6. Would be nice to get an answer from support.
If you want to have an answer from support, you should raise a Daycare ticket. Although support is quite active here, you should not expect an "official" answer from support in the forums.
Try this to persist div ids in rich text editor in cq5.6
Create a folder structure similar to "/libs/cq/ui/rte/core/HtmlSerializer.js" in apps as "/apps/cq/ui/rte/core/HtmlSerializer.js". Make sure that the folder structure and node types are as same as in libs. Then set "idAttribMode" to "keep" in "_init" function of HtmlSerializer.js. It will work
Thanks, Arya. That works!