In guitar scores I usually increase the default stem length to minimise the 
amount of manual tweaking needed to prevent fingering indications from being 
overlaid by beams (I usually put fingering indications above treble notes and 
below bass notes).

If I do this, then in single-staff polyphony, with the treble voice stems 
always up, the dot on a dotted B eighth note intersects the flag. For some 
reason, it only happens with the note B, and only when I lengthen the stems.

%%%%%%%%%%%%%%%%%%%%%%%%%
\version "2.13.30"

\relative c' {
        \time 3/4 \stemUp \autoBeamOff
        e8. g8. b8. d8. f8.
        \override Stem #'length-fraction = #(magstep 1)
        e,8. g8. b8. d8. f8.
}
%%%%%%%%%%%%%%%%%%%%%%%%%

Nick

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