Incidentally, there is another way to find the head word in examples like yours. Let me show you. Here's your original sentence again; it's a statement:
The authors’ real concern is/are not the future boundaries within the UK or the following economic recession , but the stability of the whole European Union if one if its "big three" leaves.
Now turn the first part into a question:
(1) Are the authors the future boundaries within the UK....?
(2) Is the real concern the future boundaries within the UK...?
Clearly, (1) is ungrammatical nonsense, but (2) is fine, thus again proving that the singular noun "concern" is the head word, so singular "is" must be correct.
Actually I forgot to mention 2 things, the correct version is
The author's real concern...
and, second, I was thinking about the phrase "the future boundaries within the UK...", whether there should be coordination between the Plural "boundaries" and the verb, this was my initial hesitation. Sorry for being too slow, figuratively.