Smart Sync profiles & Base Folder Creation options?

Could someone clarify what this means for me as I do not understand what is being suggested and WHY it is being suggested.

During a Smart Sync Setup I got this message:

Would you like to switch off the option to automatically create the base folders if they do not exist? This is advisable with the SmartSync Profiles as it can avoid problems where the programs thinks files have been deleted because the base folder does not exist.

Here is the scenario:
Computer A
NAS
Computer B

If Computer A creates a new folder or directory and is syncing to the NAS wouldn't you want the folder or directory to be created there so Computer B could sync to it?

Or is that not what they mean by "Base Folders"?

Thanks for the clarification.