First of all, that's a hack zsh really shouldn't have to do. It's not like it can see the output of the commands that it runs. That's the job of the terminal. To make that '%' effect work, when a command it's waiting for dies, it outputs a '%' and then as many spaces as it knows there are columns in the terminal and then a carriage return '\r'. So it uses line-wrapping to move to the next line if there's content in the current one. That's really out of scope of what a shell should be doing. It also will not work if you're not working with the shell through a terminal, but something else like a tcp connection or a serial device. What's going to happen then is that that last "line" is going to disappear in zsh. The prompt will be rendered on top of it.

Anyway, it's not just about the shell prompt. Things are just simpler and more composable when using it as a terminator instead of a separator.

Consider programs that might every now and then have to warn you about errors, like this:

cmd() {
>&2 printf "%s-error-1" "$1"
sleep 1
>&2 printf "\n%s-error-2" "$1"
}

and them being used in pipe:

cmd foo | cmd bar

using newlines as separators causes them to merge lines like so:

foo-error-1bar-error-1
foo-error-2
bar-error-2%

if one used line terminators:

cmd() {
>&2 printf "%s-error-1\n" "$1"
sleep 1
>&2 printf "%s-error-2\n" "$1"
}

then the output would be like so:

foo-error-1
bar-error-1
foo-error-2
bar-error-2

Now consider what would happen if you need to conditionalize the first line:

cmd() {
if (( $RANDOM % 2 == 0 )); then
>&2 printf "%s-error-1" "$1"
fi
sleep 1
>&2 printf "\n%s-error-2" "$1"
}

Now, if that first line doesn't output anything, you'll get a extra, blank line. So, you need to include the newline in the conditional body:

cmd() {
if (( $RANDOM % 2 == 0 )); then
>&2 printf "%s-error-1" "$1"
>&2 printf "\n"
fi
sleep 1
>&2 printf "%s-error-2" "$1"
}

Now what if you need to conditionalize the last line?

cmd() {
if (( $RANDOM % 2 == 0 )); then
>&2 printf "%s-error-1" "$1"
>&2 printf "\n"
fi
sleep 1
if (( $RANDOM % 2 == 0 )); then
>&2 printf "%s-error-2" "$1"
end
}

should the newline go in the first or second conditional body? If it's on the first, then if the first condition is true and the second is false you'll get a trailing newline (something you don't want if you're trying to have separators).

What's the solution here? The newline will have to be added only when BOTH conditional bodies run:

cmd() {
if (( $RANDOM % 2 == 0 )); then
first_was_true=1
>&2 printf "%s-error-1" "$1"
fi
sleep 1
if (( $RANDOM % 2 == 0 )); then
if [[ $first_was_true ]]; then
>&2 printf "\n"
fi
>&2 printf "%s-error-2" "$1"
end
}

What if you have a 3rd conditional error? Well, that's a new newline that will have to be output iff the second and third ran or the first and third ran:

cmd() {
if (( $RANDOM % 2 == 0 )); then
first_was_true=1
>&2 printf "%s-error-1" "$1"
fi
sleep 1
if (( $RANDOM % 2 == 0 )); then
second_was_true=1
if [[ $first_was_true ]]; then
>&2 printf "\n"
fi
>&2 printf "%s-error-2" "$1"
end
sleep 1
if (( $RANDOM % 2 == 0 )); then
if [[ $first_was_true || $second_was_true ]]; then
>&2 printf "\n"
fi
>&2 printf "%s-error-2" "$1"
end
}

Can you see how this quickly becomes unwieldy? Each new body becomes coupled to the ones before it. The third conditional needs to know about the first and second when semantically it shouldn't need to care at all! If you use line terminators, things are much simpler:

cmd() {
if (( $RANDOM % 2 == 0 )); then
>&2 printf "%s-error-1\n" "$1"
fi
sleep 1
if (( $RANDOM % 2 == 0 )); then
>&2 printf "%s-error-2\n" "$1"
fi
sleep 1
if (( $RANDOM % 2 == 0 )); then
>&2 printf "%s-error-3\n" "$1"
fi
}

This isn't just an arbitrary Unix decision. It's objectively good design.