The books don’t eliminate commas; there are no commas there. The only required comma I can think of is after a vocative ad before sentence, where there is an audible pause. Other commas may be useful sometimes (before terminal PPs after NPS, say) but none are required (well, except in Lope). Commas generally break the flow unnecessarily. So Tepan is not retaining commas, he is adding them.
Hyphens are pointless, since they just makr the fact that one word follows another. They might be hand in the case of three or more words following a ‘pi’, but those are relatively rare to justify all the rest of the parsley.
The apostrophe for missing ‘li’ after ‘mi, sina, o’ is cute and possibly useful. But some of the things Sonja says suggest that there is no ‘li’ there to be missing, that ‘mi’ attaches directly to the predicate at the formation stage. So, the apostrohe should wait for a decision on that question.
There is no ‘pi’ missing for attaching a single modifier, since ‘pi’ only comes into play with a two-word modifier. So that apostrophe is just wrong. (There is a possible hisoric case for possessive modifiers, but that is so archaic that it seems pointless to revive it, handy though it would be.)
The idea of “omitted words” has a certain appeal to a grammarian, but not enough to clutter the page with apostrophes. ‘kiwen’ as “stone, metal” is not an adjective with a missing modificand, but a derivative concrete (pun not avoided) noun. Similarly, transitive verbs without their objects are just intransitive verbs (derivational transformation are separate from grammatical ones).
I realize that these signs are not meant to be actually used in writing but only in analysis. The dange is that one comes to rely on them to read text (though God know why you would in most cases) and thus lose the grasp of how the language goes together. I think analysis is better. done by doing it in the open: this comes from this by these processes. The summary of the results is usually less informative or generally applicable.