And don't try to use the MTA map as a guide to New York City, it is woefully geographically inaccurate. But it still looks like it might be right, so it is in fact quite misleading.
The responsibility of a transit system map is to tell you about the transit system. It should do that above all else.
Do you actually live and work in New York? I'll assume not, and your attitude proceeds from ignorance of the situation.
Suppose you work at 1 Pierrepont Plaza (former HQ of Hillary Clinton's campaign, bit of trivia there) and you want to go to Nakamura Ramen on the Lower East Side. You have a subway station right outside the door with the 2345R train, but you'd be a fool to take any of those instead of walking the extra five minutes to Jay St Metrotech for the F.
You are at Broadway - Lafayette St, and you wish to head to the Flatiron Building. The nearest subway to that is the R train. You can take the 6 and transfer at Union Square... but really, you should just walk from the 6 train at 28 St.
You are staying in Fort Greene. The nearest stop is Fulton St (G). The next nearest stop is Lafayette (C). Even if you are headed to Columbus Circle (ABCD1), you might find yourself better served by by walking to DeKalb to catch the B or the Q, which are acceptably close, have more frequent service, and bypass lower Manhattan. (If you are going to the Metropolitan Museum of Art, you will instead walk to Nevins.)
You work at Union Square and live in Williamsburg. A signal problem -- residual damage from Hurricane Sandy when the tunnel was flooded -- prevents the L train from operating. What are your options for getting home today?
Your proposed universal norm actually makes a lot of sense ... for hybrid commuter rail / metro systems, such as the DC Metro, or BART, where questions like these are only minor and occasional. It is far more ambiguous for NYC.
Why do the situations you've proposed have any benefit from the MTA's map? Trying to determine which stations are near your origin or destination based on a system map is a fool's errand, particularly for as large a network as ours. If you're estimating walking times based on distance on the MTA's map, you're going to be very unpleasantly surprised.
The part of those questions that a system map can be useful for is which lines are continuous, which as I mentioned above, is best done when you can see it clearly rather than needing to read it.
I haven't heard this before. I presumed the author simply stopped updating the app. Can you elaborate?
New York City's map shows a variety of out-of-system features which the designer's map doesn't bother with: railroads, avenues, major cross streets, major bus corridors (the original identifies airport link stops but not routes), local commuter rail corridors (LIRR, Metro North), regional rail corridors (Amtrak), ferries, road bridges, tunnels, the Roosevelt Island Aerial Tram, and many more parks.
The MTA map this more effectively answers more-general questions about New York. It can tell you to walk through the park between the Natural History Museum and the Metropolitan Museum of Art. This does come at the cost of interfering with several of the more-specific questions you identified.