Too wide space between clef and first neume. Solution with setting "\set VaticanaStaff.createSpacing = ##f" makes first space too short. Clefs placed too right. Solution with: "\override Score.Clef #'extra-offset = #'(-0.75 . 0.0)"
NB. Notice that second neume is in the middle of staff in below example.

Example file:

\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\

\version "2.10.0"
\include "gregorian-init.ly"
\paper {
        #(set-paper-size "a4")
        #(layout-set-staff-size (* 18.0 pt))
        %left-margin = 7 \mm
        %line-width = 88 \mm
        indent = 0 \mm
        %ragged-right = ##t
        %ragged-bottom = ##f
        %ragged-last-bottom = ##f
        between-system-space = #(* 0.1 mm)
        between-system-padding = #(* 0.1 mm)
}

\score {
        \new VaticanaStaff {
                \context VaticanaVoice = "cantus" {
                        \override VaticanaStaff.StaffSymbol #'color = #red
                        \override VaticanaStaff.LedgerLineSpanner #'color = #red
                        \override Score.BarNumber #'transparent = ##t
                        \clef "vaticana-do1"
                        \relative {
                                \[ a \] \bar "" \break
                                \set VaticanaStaff.createSpacing = ##f
                                \override Score.Clef #'extra-offset = #'(-0.75 
. 0.0)
                                \[ d \] \bar "" \break
                                \[ g \]
                                \finalis
                        }
                }
        }
}


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