The older Bakerloo/Northern line ticket hall is actually also at street level with York Road/Leake Street, it's just well disguised because Cab Road in front of the station is elevated, and the main concourse at Waterloo is further elevated, on what you might consider the first floor as the whole station is on arches. Once the International side has been fully redeveloped, there will be ground level entrances that allow you to walk in to the underground station it on the flat, as you can see here. There is another Waterloo tube entrance across the road at the bottom of one of the Shell Centre towers, which is also on surface level, and will be reopening soon.
Here are the three official LU diagrams that I have found of Waterloo, if they are of any help.
From:
https://www.ianvisits.co.uk/blog/2015/07/12/3d-maps-of-every-underground-station-tuvw/
EDIT: I forgot about the NR station being raised up. So I suppose that yes, the Bakerloo/Northern ticket hall would be at ground level. I didn't know that the concourse was that high up though!