I discussed your question with the Elastic Cloud team and the short answer is that we will support uploading custom plugins in a future release, but you cannot upload them in alpha4. The slightly longer answer is that some of the required development work is already done, but it is not yet complete. I can't give you a more exact release date than that at this point, but the team is aware of your request and I opened an internal issue to track your feedback.
The intent of the note in the docs was to prevent a potentially frustrating scenario where the UI seems to support adding new versions of ES to Elastic Cloud Enterprise, but when you try it with one of the regular ES Docker images, it doesn't work.
Nik