For example, Zuck says he runs the company via Messenger - but a chat tool without selective muting/@mentions (or equivalent) is bound to be messy at the scale at which he's working. Similarly, Facebook's group chat isn't the best archival tool, nor does it support features like merging posts or transferring them from one group to another.
He does; he’s a bit of an outlier in how he can handle intense communications, but Messenger at his scale is not less manageable than e-mail — it mainly encourages extreme brevity.
The information filtering is done using groups and notification that allow everyone to target their attention; his is focused on high-level groups that distill details from other working groups.
That doesn't mean that Google Apps is the best tool, or even that it works well for everyone, but it means that people are willing to put up with a less than perfect solution that's integrated with the rest of the company.
Of course in the above FB scenario this is not a problem because they're the vendor.
It actually is. The vast majority of essential information is in there; HR tools, some IT stuff is based on integration with the Facebook codebase.