There are a few categories of words in your list, so I'll break it down into the categories...
1. Not an uncommon word
In this category, you'll find that the words aren't actually uncommon, just situational. You'll usually hear these pop up occasionally in TV shows and movies, spot them in books, etc.
Words: quaint, mahogany, curtsey, tidings, brawny, stench, rickety, menagerie, beckon, throng, swoon, tattered, malady, frill
2. Context plus root gives it away
Words here are not themselves common, but they bear close resemblance to common words, and then context clarifies them from there.
Special subcategory: "-er"
Words: tiller ("to till the land"), upholsterer ("upholstered"), pilferer ("to pilfer")
Other words: piscatorial ("pescatarian" or "pisces", both have to do with fish), consignment ("to consign"), wolfishly ("-ishly" means in a way that is like), meekness ("meek" is a common word), trenchant ("trench" is an intentional hole for defense or other uses)
3. Appears in set phrases
These words are ones that people might not know the meanings of in isolation, but they survive in a few specific phrases, and context might get you there from that point.
Words: myriad ("in myriad ways"), canter ("at a canter"), scullery ("scullery maid"), asunder ("torn asunder"), teem ("to teem with life"), peal ("a peal of thunder"), gossamer ("on gossamer wings")
4. Unusual words but not unheard of
Here are words that most adult native English speakers will have at least heard a few times, and they're pretty clear from context.
Words: filament, breech, demur*, pith, paunch, compunction, balustrade, scruple+, cachet, arrear+
* demur is more likely to be heard, and the spelling doesn't make it obvious - it's "deh-mewer", not "dee-mer".
+ scruple and arrear are usually seen in plural as scruples and arrears
5. Very unusual
The remaining words are unusual enough that a lot of native English speakers either won't know them, or will at best be able to guess at them.
Words: fain, coppice, lee-dyed, provender, purloiner, asseveration, gainsay, staid, lacquey, flambeau, jalousie
Some of these might be old spellings (fain - feign? lacquey - lackey? jalousie - jealousy?). A few are modifications of uncommon words (purloiner from purloin, in particular). I personally know purloiner, gainsay, and staid. The others, I can only guess at.
To answer the question
How do native English speakers know these words? It's a combination of context clues and past exposure, just as in any language.
A few of these, I mostly heard through TV shows like The West Wing or Frasier, where the characters having a large vocabulary is very intentional. In some of these, there would be a character who doesn't know the word, so that the other character can explain the meaning to them, and thus to the audience.
A few such words include "torpor", "promulgate", "onomatapoetically", "filibuster", "acalculia", "estuary", and "redoubtable" (all from West Wing) - I knew some of them already.
Tiller
out of context -> I think of boats. But Dickens might have used it in relation to either boats or agriculture. Try to make sure you use editions with modern spelling, as that will remove one source of uncertainty. (UK English speaker.)