The default value of $IFS contains the SPC, TAB and NL characters (also NUL in zsh, other shells either remove the NULs or choke on them). Those (not NUL) also happen to be IFS-whitespace charactercharacters¹, which are treated specially when it comes to IFS-splitting.
If the output of cmd is " a b\nc \n", that split+glob operator will generate a "a", "b" and "c" arguments to ./input. With IFS-white-space characters, it's impossible for split+glob to generate an empty argument because sequences of one or more IFS-whitespace characters are treated as one delimiter. To generate an empty argument, you'd need to choose a separator that is not an IFS-whitespace character. Actually, any non-whitespace character but SPC, TAB or NL will do (best to also avoid multi-byte characters which are not supported by all shells here).
Those " are part of the shell syntax, they are shell quoting operators. Those " characters are not passed to input.
¹ IFS whitespace characters, per POSIX being the characters classified as [:space:] in the locale and that happen to be in $IFS though in ksh88 (on which the POSIX specification is based) and in most shells, that's still limited to SPC, TAB and NL. The only POSIX compliant shell in that regard I found was yash. ksh93 and bash (since 5.0) also include other whitespace (such as CR, FF, VT...), but limited to the single-byte ones (beware on some systems like Solaris, that includes the non-breaking-space which is single byte in some locales)