I don't know if Jackson has discussed this himself, but Richard Armitage (who played Thorin) has been asked this a couple of times, and provides his thoughts in, for example, a 2015 interview with Yahoo Movies:
Why do you think these scenes were cut? For length?
Partly that, but sometimes you can repeat themes. There were a lot of characters who had to finish of their stories, for example the Tauriel/Thranduil storyline had to finish. Playing a funeral scene on top of that is just overloading the end of the movie so to be honest I wasn’t disappointed that it got cut. The end of the film felt right without it.
Say what you will about the emotional poignancy of the scene, but it's not actually very important to the narrative, or to any of the main character arcs. The Hobbit is principally a story about Bilbo, and Thorin's funeral doesn't advance his story in any meaningful way. Nor does it really advance the stories of Tauriel or Legolas (the main tertiary arcs).
It does serve to conclude the story of Thorin, the secondary character arc of the series, but his death is established in an earlier scene (which was added in response to this scene being cut, as Armitage mentions earlier in the same interview):
I know that when the decision was made to take that out of the final movie was made [sic] there was a little scene added where you see the dwarves on the waterfall and they kneel around the dead body. That was an addition because the funeral was cut.
Thorin's arc is adequately closed with the scene they added; I'm not going to argue that the funeral wouldn't have been a better way to end his story1, but it's not an unreasonable trade-off, given the requirements of the other stories.
Aside from that, it mainly serves to resolve some unanswered continuity questions (as you point out in your question) that aren't, ultimately, that interesting, except to the kind of obsessive loons who buy the extended editions.
1 Which is probably why the scene was restored for the extended edition