Hi Jesse
It's mainly about the interface, workflows, resource limits, and branding. Yes, you can do just about the same thing in both at the language level. Wolfram Programming Cloud (WPC) has an interface that emphasizes deployments and it also provides reporting focused on deployments. Mathematica Online is more focused on extending the Mathematica experience to the cloud and sharing content with others. We, as a company, are trying our best to match the correct people (markets) with the correct interface to the Wolfram Language.
This is true for a few of our unreleased products as well. Data Science Platform has an interface designed around the idea of data-in --> Interpret/Clean --> Automated Analysis or custom analysis --> create/schedule report --> deploy report.
As these products mature and leave the beta phase there will be more unique features added.
Thanks for the question!
~ Clayton