An override for Stem.stem-begin-position only affects unbeamed stems, which is at least undocumented.
Maybe better to let it work for beamed stems as well.
\version "2.19.52" { \override Stem.stem-begin-position = 4.5 \stemUp c''8[ d''] \autoBeamOff c'' d'' }
Diff:
Some discussion here:
http://lists.gnu.org/archive/html/bug-lilypond/2016-12/msg00016.html
Our regtest input/regression/stem-length.ly avoids testing beamed stems.