Any way to set preferences programmatically?

Use (find-system-path 'pref-file) to find the preferences file.
Then you need to look through to find the keys you need.

Welcome to Racket v8.12 [cs].
> (find-system-path 'pref-file) 
#<path:/Users/soegaard/Library/Preferences/org.racket-lang.prefs.rktd>

% head -5  /Users/soegaard/Library/Preferences/org.racket-lang.prefs.rktd
(
 (|plt:DrRacket 7.7-splash-max-width| 996)
 (|plt:DrRacket 7.7.0.4-splash-max-width| 996)
 (|plt:DrRacket 7.7.0.7-splash-max-width| 993)
 (plt:framework-pref:drracket:home/end-is-beginning/end-of-document #t)

Most settings are under drracket not DrRacket.

% grep drracket  /Users/soegaard/Library/Preferences/org.racket-lang.prefs.rktd | wc -l
     114
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