Where is the data stored?
The data is stored on your Atlassian instance and backed up by Atlassian
Are there any known limitations?
Yes, due to the nature of the cloud there are still some limitations, see Known limitations
Can we secure the native and/or other vendors custom fields using protected fields?
No, there is no way to interact with other fields available in the platform hence we can not interfere with other field types then our own build types.