do we have documented a detailed description of the the files and directories (groups) operations in this case. For example, what happens if I move a directory on DEVONThink To Go or create a new file etc.
No, there is no whitepaper on what is happening in the internals of a database in DEVONthink To Go. It is no place anyone should be getting into, even if it was possible.
Also, one of my use cases was the use of company confidential files that cannot be taken out of OneDrive: I have successfully setup a database on top of the files of interest and worked successfully for a while but based on what you say, if I sync this database with the mobile devices it will take the files out of OneDrive and store them locally on the device. Is this correct understanding?
It will not take the files out of OneDrive. However, a copy would be stored in DEVONthink To Go on the mobile device. This would likely be a violation of your company’s security policy.