The question is not about what the _lone word_ "user" means. That's obviously not specific enough to have a single definition.
The question is what does "3 million people who use our web-based apps" mean.
A simple truth test: Are there "3 million people who use [their] web-based apps"? Absolutely not. Not under even the most remotely reasonable definition.
It does? Says who? This is your definition of a user. That's fine, but it doesn't extend to being a common one.
Unless of course you delete all the accounts of people that have registered for your service but aren't using it as often as you'd like.