Semicolon: Always required before conjunction if internal punctuation follows, even if no ambiguity?

Is the semicolon in the following sentence necessary? Is it preferable? To me, it seems that there would be no ambiguity if the semicolon were replaced with a comma, but the writer insists that a semicolon is required because the part after “or” includes commas.

In that factory process, the production materials can be delivered to the line as is; or a substance that is immune to the production materials and lubricant, such as B1, B2, and B3, may be included.

I wonder what "rules" there are concerning this type of usage.

The Chicago Manual of Style, for example, says at item 6.59:

An independent clause introduced by a conjunction may be preceded by a semicolon, especially when the independent clause has internal punctuation.

Maria had determined to question the ambassador; but bodyguards surrounding him, as well as the presence of dancing girls, prevented him from noticing her.

But, again, would there be any ambiguity at all in changing the semicolon after "ambassador" to a comma? If not, is the use of a semicolon in such a case just a matter of individual preference?

There are no strict rules governing the use of semicolons, and few consistent conventions.

By and large the semicolon is used when you want to mark a disjunction as 'stronger' than one marked by a comma but not so strong as one marked by a full stop. One fairly routine use, for instance, is to distinguish successive list items which themselves require articulation with commas. Otherwise, use of the point is governed mostly by the author's professional sense of the balance to be struck between the amount of material he wants to pack into one sentence and the mind-numbing effect of too many commas.

I suggest, as a rule of thumb, that the semicolon should be treated as a hinge on which a sentence turns: it should be used to mark a change of direction between related but in some way contrasted propositions. That contrast may be of any sort—a negation, a concession, a more detailed recapitulation, or whatever—but it has to be there for the semicolon to be required, and the two propositions should be so constructed that they mark the contrast as clearly as possible.

(For this reason I strongly dispute the suggestion that a coordinating conjunction should not follow a semicolon. The semicolon marks the turn, but the conjunction tells you in what direction the sentence is turning.)

Your second example seems admirable to me: A) heroine sets an objective; B)ut such and such agents conspire to cause her failure.

Your first example, however, is not so pleasing. The context does not demand a semicolon, because the contrast does not lie between the two clauses but between the second clause and the single brief phrase "as is". Everything before that phrase belongs, properly, to both clauses. What the author means may be more intelligibly expressed with a simple either ... or construction:

In that factory process, the production materials can be delivered to the line either as is or with an added substance, one that is immune to the production materials and lubricant, such as B1, B2, and B3.

^†<rant>Contemporary usage, however, does not much like texts more complex or subtle than can be encompassed in a tweet , so the semicolon is rapidly becoming replaced by a proliferation of full stops.</rant>

@StoneyB 's excellent answer and suggested rewrite are effective because they bring the scope of conjunction down to a lower level. In the original sentence, you are coordinating two full clauses: The production materials can be delivered... and A substance that is immune.... In the suggested revision it is two adjuncts which are conjoined: as is and with an added substance...

If you want to rewrite it with full clause coordination, modify the second clause to include locative inversion; this puts the predicate up front and lets the reader pick up on the scope of the conjunction right away:

In that factory process, the production materials can be delivered to the line as is, or there may [also] be included a substance that is immune to the production materials and lubricant, such as B1, B2, and B3.

Personally I like the adjunct coordination version better, but it's good to know what options you have.