I'm sorry this is becoming a game of whack-a-mole but I have found another instance of an alternate classloader not being propagated properly similar to https://github.com/spring-projects/spring-boot/issues/27133.
The offending line can be found here: https://github.com/spring-projects/spring-boot/blob/dfe91be885a8623db1093d6a823605a5bc5159fd/spring-boot-project/spring-boot/src/main/java/org/springframework/boot/sql/init/dependency/DatabaseInitializationDependencyConfigurer.java#L165
This is leading to a ClassNotFound exception on the FlywayDatabaseInitializerDetector class.
Comment From: jaminh
It appears after this fix I was able to get spring boot running with an alternate classloader. The only small issue outstanding is the LoggingSystemShutdownListener in the spring cloud project. I am able to work around that issue but I proposed a fix here https://github.com/spring-cloud/spring-cloud-commons/pull/972.