This can be reproduced with Gradle, but you don't need a Gradle project for this. When running from a normal console:
$ gradle
Starting a new Gradle Daemon for this build (subsequent builds will be faster).
:help
...
Total time: 2.014 secs
Now if I repeat it, the daemon is reused, so the first message is gone and the "build" goes much faster:
$ gradle
:help
...
Total time: 0.495 secs
By comparison, when run from Emacs M-x compile, Gradle starts daemon every time, so all builds look like the first example above. However, if daemon already exists (e.g. created by console run above), it will not be killed.
File '~/.gradle/daemon/VERSION/daemon-PID.out.log' for daemons spawned after M-x compile ends with this line:
Daemon vm is shutting down... The daemon has exited normally or was terminated in response to a user interrupt.
When daemon is allowed to exist (e.g. when run from a normal console), log receives this message instead:
... Daemon is idle, sleeping until state change or idle timeout at ...
Additionally, I checked several other ways to run process from Emacs:
* M-x eshell: daemon is killed, as with M-x compile
* M-x shell: daemon works properly
* M-!: daemon works properly
So, it seems that Emacs has a way to keep daemons alive / not kill them, but it is not used in compilation mode.
Paul