One example when you have to use \score explicitly is when you
have several scores in the same .ly file (for example several movements)
and want to specify a separate title for each of them. Then you have to
put the \header block within the corresponding \score block, so LilyPond
realizes what belongs where. Same if you want to specify the tempo used
in the MIDI file for each separate score. Example:
\version "2.6.0"
\score{
\relative c'{ c d e f | g1 | }
\header{ piece = "First movement" }
\layout{}
\midi{\tempo 4=80 }
}
\score{
\relative c''{ g e f d | c1 | }
\header{ piece = "Second movement" }
\layout{}
\midi{\tempo 4=120 }
}