Actually, the accuracy of some of the maps in The Atlas of Middle-earth has also been questioned. I think that in general they are good, though there are scattered errors or inconsistencies.
The closest thing we have to an authoritative map of Beleriand by Tolkien himself is the map found in HoMe XI, The War of the Jewels. Like all the HoMe material, there are parts of it that must be considered outdated - but this is chiefly in regard to the names on the map. The actual geography can be considered almost completely canonical.
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