For the film, it is really the pacing issue that is most crucial: FotR is already a long and complicated movie, and it really doesn’t have a second to spare on unnecessary scenes. And, unlike a book, movies can’t really be digested slowly (especially not in a theater). The Bombadil scene is a small oddity in the book but it could have been a fatal flaw in the film, disengaging audiences before we even get to Bree.
I think Bombadil could have been effective later in the trilogy - where the fact that the Ring has no affect on him would carry more dramatic weight, and where the “tonal inconsistency” would be surprising and refreshing rather than confusing. Perhaps shortly after meeting the Ents - it would strengthen the idea that Bombadil is vastly powerful (even compared to Sauron) but aloof from human/elf/dwarf concerns.