So, this is a general problem with the general-column scheme function...
Following up the mails on lilypond-user, I can now confirm that the \center-
column markup command has an issue with the extents of the stencil it
returns.
It seems that the returned markup ignores all extents left of its center, so
the first half of the column-markup will overlap with previous markups. A
simple test case is attached:
\markup \line {
\center-column { \line {a b} \line {c} }
\vcenter {"+"}
\center-column { \line {a b} \line {c} }
}