That question has a more specific answer: According to Gould, one of them is
not just “more natural” but*correct*, and the other is not just “less natural”
but*incorrect*.;)
When dividing any note duration, there is a specific formula when to move from
one sub-duration to the next smaller sub-duration (e.g. in tuplets of varying
number). Those rules, of course, apply equally to the note-glyph used in the
denominator of a time signature. Naturally, Lilypond can’t force someone to use
the “correct” engraving — but that doesn’t change the fact that there are clear
rules as to how to properly engrave such things!