The point isn't that one should reinvent the way that Tomcat is started, but that Spring Boot (by default) is using action at a distance and runtime reflection which have serious downsides if you want to understand what's actually going on because you're a) new to the technology, or b) have to debug some weird edge case.

The alternative is using explicit, reflection-less code - which you can do even with Spring, although it's experimental: https://github.com/spring-projects-experimental/spring-fu