It does honour the sync setting, however there are two types of sync.
Setting to manual simply disables the "full" sync which both pulls the data from the sync target and pushes any new data to it - this is the sync that runs periodically and is disabled from running by setting it to manual. However I believe this also runs on startup regardless of setting to make sure the client is up to date to prevent any conflicts.
There is also a "push" sync which happens whenever a note is created or modified and pushes changes to the target but does not download. This one is not disabled by setting it to manual.
If you don't want it to sync at all you need to select (none) as the sync target.