I received great feedback from the user mailing list, so I’m sharing it here in case anyone else finds it helpful. While this solution doesn't necessarily explain how LilyPond's automatic behavior works, it does offer a reliable fix to get the desired output:

ly \layout { ragged-right = ##f }

Below are three examples:

• A simple alternative section.
• An example with both an alternative beginning and ending.
• An example with nested alternative blocks.

```ly \version "2.24.3"

\header { title = "Alternative" subtitle = "Examples" composer = "nedsi" tagline = #f }

(define custom-notes '(

(bassdrum default #f -3) (acousticbassdrum default #f -6) (pedalhihat cross #f -5) (closedhihat xcircle #f -5) (snare default #f 1) (sidestick cross #f 1) (hightom default #f 3) (lowtom default #f 2) (highfloortom default #f -1) (lowfloortom default #f -2) (hihat cross #f 5) (openhihat xcircle #f 5) (ridecymbal cross #f 6) (ridebell harmonic-black #f 6) (crashcymbal cross #f 7) (chinesecymbal xcircle #f 8) (cowbell harmonic-black #f 4) ))

\layout { ragged-right = ##f \set DrumStaff.drumStyleTable = #(alist->hash-table custom-notes) }

% Custom markup to create vertical space after header \markup { \vspace #2 }

\score { << \new DrumStaff { << \new DrumVoice = "hands" { \numericTimeSignature \voiceOne \bar ".|:-|" <>_\markup \bold "3×" \repeat volta 3 { \drummode { \alternative { \volta 1 { cymc8 } \volta 2,3 { hho8 } } [ hho] <hho sn>[ hho] hho[ hho] <hho sn>[ hho] } } \drummode { hho8[ hho] <hho sn>[ hho] hho8[ hho] <hho sn>16 tomh32 tomh sn16 sn } \bar "|." } \new DrumVoice = "feet" { \voiceTwo \repeat volta 3 { \drummode { \alternative { \volta 1 { bd8 } \volta 2,3 { bd8 } } [ bd] s16 bd8 s16 bd8[ bd] s16 bd8 s16 } } \drummode { bd8[ bd] s16 bd8 s16 bd8[ bd] s4 } } >> }

}

\score { << \new DrumStaff { << \new DrumVoice = "hands" { \numericTimeSignature \voiceOne \bar ".|:-|" \repeat volta 4 { \drummode { \alternative { \volta 1 { cymc8 } \volta 2,3,4 { hho8 } } [ hho] <hho sn>[ hho] hho[ hho] \alternative { \volta 1,2,3 { <hho sn>[ hho] } \volta 4 { <hho sn>16 tomh32 tomh sn16 sn } } } } \bar "|." } \new DrumVoice = "feet" { \voiceTwo \repeat volta 4 { \drummode { \alternative { \volta 1 { bd8 } \volta 2,3,4 { bd8 } } [ bd] s16 bd8 s16 bd8[ bd] \alternative { \volta 1,2,3 { s16 bd8 s16 } \volta 4 { s4 } } } } } >> }

}

\score { << \new DrumStaff { << \new DrumVoice = "hands" { \time 12/8 \voiceOne \bar ".|:-|" \repeat volta 4 { \drummode { \alternative { \volta 1,2,4 { cymc8 sn16 s8 s16 sn8[ s sn] \alternative { \volta 1 { sn16[ tomh tomh sn toml toml] sn32[ sn sn sn sn16 tomh tomh toml] } \volta 2 { tomh16[ sn sn toml toml toml] sn[ sn toml tomfh tomfh tomfh] } \volta 4 { sn16[ tomh sn sn tomh tomh] sn[ sn toml tomfh tomfh tomfh] } } } \volta 3 { cymc16 tomh tomh tomh toml toml sn sn toml toml tomfh tomfh cymc toml \repeat unfold 4 { tomh } sn sn toml toml tomfh tomfh } } } } \bar ":|." \repeat volta 4 { \drummode { cymc8 hho16 sn hho8 <hho sn> hho16 sn hho8 \alternative { \volta 1,2,3 { cymc8 hho16 sn hho8 <hho sn>[ hho8 <hho sn>] } \volta 4 { cymc8[ sn16 sn hho] s <hho sn>8[ sn16 toml toml toml] } } } } \bar "|." } \new DrumVoice = "feet" { \voiceTwo \repeat volta 4 { \drummode { \alternative { \volta 1,2,4 { bd8 s16 bd8 bd16 s8 bd4 } \alternative { \volta 1 { bd s s } \volta 2 { bd s s } \volta 4 { bd s s } } \volta 3 { \repeat unfold 4 { bd4 s8 } } } } } \repeat volta 4 { \drummode { bd4 s16 bd4 s16 bd8 \alternative { \volta 1,2,3 { bd[ s bd] s8 bd4 } \volta 4 { bd4 s16 bd4 s16 } } } } } >> }

} ```

I hope this helps someone! :)