True, but if there is a box of books as well as some suitcases, then the 'rule' appears to be, "When two subjects are joined by as well as, together with or a similar expression, the verb is usually singular if the first subject is singular" (Swan (2005) Practical English Usage (3rd edn), OUP. This is a rule more honoured in the breach, as I suggested in post #2.
A further point is that it is probably more normal for most speakers, if they don't use 'and' instead of 'as well as' in the first place, to put the 'as well as ...' at the end:
A is under the table, as well as B. Even more natural would be to start with a 'there's/are':
There is a box... as well as some suitcases under..
There are some suitcases as well as a box ...
To make matters worse, the test writer has perversely chosen 'A box (singular) of 'books (plural) to make it more difficult to to choose the officially correct 'is'. There seems to be a deliberate attempt to catch the learner out in a sentence which native speakers don't agree on, and which they probably wouldn't utter in that form anyway.
The use of the word 'usually' in the 'rule' renders the exercise even more pointless, quite apart from the ambiguity emsr2dt noted.