Not sure if it's hidden on purpose, but it has a @public annotation and the sap.m.MessageBox mentions it multiple times. For example:
(...) dialog is closed by calling
sap.m.InstanceManager.closeAllDialogs().
So I was curious what kind of module the InstanceManager is but couldn't find it in the API reference.
https://openui5nightly.hana.ondemand.com/#/api/sap.m.MessageBox/methods/sap.m.MessageBox.alert
InstanceManagerThe item sap.m.InstanceManager is displayed in the Tree.
No results found.

https://github.com/SAP/openui5/blob/master/src/sap.m/src/sap/m/InstanceManager.js
Hello @boghyon,
Thank you for sharing this finding. I've created an internal incident 1880599705. The status of the issue will be updated here in GitHub.
Regards,
Nayden
Fix should become visible on openui5nightly after the next nightly build.
Most helpful comment
Fix should become visible on openui5nightly after the next nightly build.