I recently watched the Return of the King film with my family, and the (second-last) ending, where the "last ship" sails from the Grey Havens, prompted the thought that has led to this post.
Technically, the "Last Ship" is the one which Cirdan and Celeborn take some time in the Fourth Age. It must be after year FoA 171, as a note in the
Thain's Book - transcribed from the
Red Book of Westmarch says that Cirdan might still live at the Grey Havens. Arwen also has the opportunity to depart after Aragorn's death in FoA 120.
While there are some elements in Tolkien's evolving legendarium which are inconsistent with the overall lore, I don't think the examples you've picked fit the bill very well. It seems to me that the theme of exceptionalism is usually used purposely to illustrate deviation from what is
normal, natural, the proper order of things and serves rather to strengthen the underlying motifs. This can be as the result of sorcery, the grace of the Valar, or Eru's personal intervention ("providence").
I think there's also a world of difference between "things we don't necessarily understand about Middle-Earth because they aren't made explicit" and "things which contradict established lore in Middle-Earth."
I think that Beorn, and the giants from The Hobbit are better illustrations.
*Gollum is a unique adversary, with his ability to live in the dark eating only fish and Goblins, his toughness, resilience, and ability to strangle, his ability to relentlessly follow the Fellowship and Frodo;
These are functions of the corrupting influence of the Ring, and serve that motif.
*Tom Bombadil - nuff said - but also Goldberry, and Old Man Willow on the borders of The Shire;
Bombadil might be Eru or the author inserting himself into the story; he is certainly an exception. Goldberry is a "not-known" but we might reasonably infer that she is a maia; Old Man Willow is consistent with the remains of the Primeval Forest, and the notion of "Ents becoming tree-ish/trees becoming ent-ish."
Again, illustrating the unnatural effects of sorcery.
the White Tower too, with its unique Palantir;
I'm not sure whether you're referring to the Palantir of Minas Tirith or in the Tower Hills.
*Gandalf's (one-time) knowledge of every spell, and the suggestion that the Mouth of Sauron is a sorcerer, yet the apparent lack of spell casting by anyone in the story but Gandalf and Saruman;
Well, the Witch-King, Galadriel and Sauron all "do magic," and I'm not sure that we're required to see the Mouth of Sauron do magic "on-screen" for his authenticity as a sorcerer to be confirmed.
*Boromir's journey across tracts of wilderness to find his way to Rivendell just in time for the great Council, in the same world where Gimli doesn't know that Balin and all his fellow-Dwarves lie dead i Moria;
Boromir's journey is exceptional.
*And what I was reminded of the other day - Frodo and Bilbo, neither an Elf, both nevertheless travelling to the Undying Lands on a ship from the Havens; and despite Cirdan having sailed, Sam - by repute - later taking the same journey on the straight road; and later still, Gimli sailing with Legolas to the Undying Lands.
See the note above regarding the date of the Last Ship. And the Gimli thing is definitely an "it is told" or an "if this be true" type thing; it is purposely placed in the region of speculation.
Although there are things in Middle Earth that are typical, even "rules" - eg the difference in the "afterlife" of Elves and Men (and Hobbits sharing, one assumes, the Gift of the One to Men); and various orders of being - the story of LotR is full of contradictions of these.
Yes, and they are a function of divine grace or they are unnatural; deviant; contrary to the proper order of things
I think consistency in a FRPG setting, in the sense of "a place for everything, and nothing out of place* is overrated. LotR is driven by departures from such consistency at just about every point.
I can't say I agree with your premise, or the examples you've used to illustrate it.