One off the positives is that you can create one Ember App and control what is build en uploaded depending on what and where to you are deploying.
ember deploy customer1
ember deploy customer2
See also Ember-cli-deploy, different build targets - #2 by Spencer_Price
We use ember-cli-deploy on every project and get value from it. With your App per customer you will secure with ember-cli-deploy in Git how each customer is deployed.
It is how I would solve your case. There are many other ways. @dknutsen can you help with some tips here?