These are examples of elision: words that are repeated have been deleted.
The underlying sentence for "She hugged and kissed her mother" is "She hugged her mother and she kissed her mother", for "Will you have that with or without syrup?" is "Will you have that with syrup or will you have that without syrup?", and for "Four and five are the square roots of sixteen and twenty-five, respectively" is "Four is the square root of sixteen and five is the square root of twenty-five" (with "respectively" added to clarify that the first two numbers relate directly to the second two numbers in the same order -- a logical and probably obvious addition, but necessary because writers don't always get it right, so adding the word might ensure that they check what they've written).
"With or without" isn't a "super-preposition" (not a bad name for it) but a set phrase used in a certain way.
For "She rescued and provided shelter for the cat", the underlying sentence is "She rescued the cat and she provided shelter for the cat". "The cat" is the object of the first verb and of the preposition (it's part of the prepositional phrase, not the object of the prepositional phrase). Because of this asymmetrical status, the sentence may be considered poor style by some (I don't think it's a problem), just as some complain that "She sang to and provided dinner for the cat" isn't good style because the prepositions are different (just a vague memory from a post on an English usage Usenet or Google Group).
Tree diagrams are merely tools for analyzing a sentence. They don't deal with reality (nobody uses them when speaking or writing, and nobody but a linguist trained to use them thinks about them outside of language class).
See: Chomsky, Noam (1957), Syntactic Structures, The Hague/Paris: Mouton
Syntactic Structures is an interesting book, and it helps when parsing a sentence to visualize a tree diagram. It works for short and relatively easy-to-understand sentences like these. I never used tree-diagram analysis outside a linguistics class, just as I never diagrammed sentences outside an English grammar class.