Ben, I have been having the same issue and am thinking this is a bug, it also seems like the documentation could be a little better to explain why some fields are the way they are and where the defaults are.
Doing a quick search in some of the directories for the amazonaws.com I found the following file and the line below.
# endpoint: 'https://s3.amazonaws.com' # default: nil - Useful for S3 compliant services such as DigitalOcean Spaces
it looks like if this line is in the active gitlab.yml (I assume it is a config for the some part of the system) it should set the default to amazonaws.com when left blank. What we are seeing is when we enter in a different address it is simply appended to the default.
Gitlab is huge and not being any good at Ruby it is pretty much beyond most of my grasp but I will keep poking about and maybe if we change the default value to point to digital ocean that may help.