S-V agreement: It is not clear what is/are meant by A and B

You are correct: it should be is. The writer perhaps mistakenly treated by “the front unit” and “the central element” as the subject, which in fact is singular what. The by phrase is an adverbial constituent of instrument or similar.

Now it could be argued that what should be plural in this clause, which is in theory possible. However, it could just as well be analysed as singular: the clause could be considered elliptical, where parts have been omitted for brevity, as it is normally done:

In paragraph 6, it is not clear what is meant by x and [what is meant] by y.

Moreover, the phrase what is meant is almost universally used in the singular and could be said to be idiomatically fixed. The plural sounds odd to my ears.

I won't argue with StoneyB's and your analyses of why the verb should be "are" instead of "is", or your feeling that "what is meant" sounds more natural, but I will say that Fowler would probably advise the writer to recast the sentence so that it isn't such a bad one. It's "bad" because it draws attention to itself, not because it's ungrammatical. Grammaticality is a poor basis for choosing how a sentence should be written when the result is such a sore thumb.

In paragraph 6, it is not clear what “the front unit” and “the central element” mean.

This is much better and two words shorter.

In paragraph 6, what “the front unit” and “the central element” mean is not clear .

This is much better than the original and three words shorter. And it suggests that it might be possible to say

In paragraph 6, it is not clear what is meant by “the front unit” and “the central element”.

I'm sure that Huddleston and Pullum would rush to its defense as a standard and acceptable sentence. I'm not sure that I wouldn't agree in this case.

MWDEU (p. 58) says:

"Mixed usage occurs when the subject what in the clause is singular but the predicate nominative is plural. In such cases, the main verb tends to be plural":

"What bothers Professor Teeter most are the guesses, hunches, speculations, and fancies in which many language shamans like me indulge -- Safire 1984".

and:

"What is most striking about Johnson is the vigor of his ideas, the variety of his knowledge, the forcefulness of his conversation -- J. C. Mendenhall, English Literature, 1650-1800, 1940 (in Bryant)".

I'd say that the structure of the original sentence is different from Safire's: no plural noun phrases immediately after the verb, but a past participle (meant), which, we now know, is always an adjective.

In paragraph 6, it is not clear what the meanings of “the front unit” and “the central element” are.

is perfectly grammatical and unexceptional. I'm not sure, however, that this can be said of

In paragraph 6, it is not clear what are meant by “the front units” and “the central elements”.

Google Ngrams Viewer shows that "is meant by the terms" is and has been used significantly more than "are meant by the terms" (almost zilch) [Only 5 words allowed for an Ngram search].

I conclude that the sentence should be:

In paragraph 6, it is not clear what is meant by “the front units” and “the central elements”.

simply because of the syntax: It's not typical and it seems to require a special usage rule.