I'm not saying you shouldn't be able to modify the way the source appears, even going so far as saying "there should be a new variable here." I'm just saying that those modifications should live in the layout document, rather than in the source itself.
Think of it like an archivist restoring a painting. First, they add a (removable) clear-resin barrier layer; and then they do restoration work on top of that barrier. In essence, rather than the paint they're adding becoming part of the painting, it instead becomes part of a "wrapper" for the painting, which can always be "unwrapped" back to the source.
Except this analogy isn't perfect, because you can only override a painting point-by-point; whereas a layout document can "losslessly" cut a linked source up into chunks and put each chunk in a different place, repeat chunks, insert things between chunks, etc.
A better analogy, actually, might be a DAW project. The input audio samples are immutable; the DAW project takes samples from the inputs, applies changes to those samples, and then sequences the results.
And note that a large part of the point of this workflow (in desktop publishing, at least) is that the upstream can continue iterating on the linked document as the downstream lays it out. Those changes may break the downstream layout, but they usually don't, because the downstream layout has usually been defined by constraints.
For example, in a newspaper article, if the source-text of the article gets more wordy, then up to a point, the layout engine just packs those same paragraphs tighter on the page it already decided they appear on, while keeping the paragraphs that appear on the next page spaced as before, and not allowing any lines from the paragraphs on page A to migrate to the flow-box on page B. But at a certain point, it switches strategies, moves an entire paragraph from A to B, and then relaxes the spacing of A back down. At that point, the layout may have been broken (because now B might be either too long to fit its flow-box, or unreadably tightly-spaced.) But that happens surprisingly rarely, compared to constraint-based reflow "just working" to absorb linked-document changes. (And note that either the writer or the layout designer can aid this process by inserting explicit page/section breaks that add weights to these constraints, to keep reflow from flapping lengths around.)
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Note that everything I'm talking about is already how a very domain-specific kind of Desktop Publishing already works: "engraving", a.k.a. sheet-music publishing. The score itself (the thing that contains information that could be converted to MIDI) and the engraving details (the way to present the score to a human) are kept separate in most engraving-tool formats.