"Windows" updates section:
In this case you have MetaData imported and only required vendor/updates are selected, so Windows Assessment scan executes on managed windows computers based on list of updates that you've imported via MetaData, therefore you got appropriate list of Bulletins/Updates and their compliance state.
Windows (Microsoft Data) section:
In this case, 'Windows Update' service asks Microsoft to get currently released/applicable updates (not based on MetaData that you've imported but it's like when you manually open "Windows Updates" on windows OS and start "Check for Updates".
When Windows Updates check is done on client side, they will send currently available updates list for them to NS, so admin on NS side, can see all available updates in "Microsft Updates" report under "Windows (Microsoft Data)" and ditribute them via mouse right click.