-L and -I are specified at compile time, so if you distribute/deploy a binary the runtime doesn't have to care (except in the case of dynamic linking - eek!)

$CLASSPATH is purely runtime, so it's all the fun of dynamic linking, all the time. Monolithic shaded JARs can solve this problem but introduce some of their own.

So someone has already gone to the effort of specifying them. In that case the analogous java situation is downloading a packaged jar and running java -jar mything.jar