For what it's worth, I find experimentally that you CAN ignore this dialog, and just click OK three times per build. Actually installing Java does not appear to be necessary for the build to complete.

Still present in 5.3.4. Of course maybe "fixed in future release" means some more future release than that.

Every other bug system on the planet provides a little more detail, such as WHEN the bug was fixed, so we can get some clue as to which release it might appear in. And maybe even some comments from the engineers like "yeah, you can ignore that pop-up" or "oops, yeah, you need to actually install Java in order to build for WebGL." It's really frustrating how Unity's bug system doesn't provide for any such feedback, leaving us just as much in the dark as we were before finding the existing report.

You should check to see if java AND javac is installed properly.
The easiest method is via brew
> brew cask install java

then check your ENV variables for JAVA_HOME:

export JAVA_HOME=/Library/Java/Home
export PATH=${PATH}:$JAVA_HOME/bin

then logout/login or restart and check if everything works:

>java -version
java version "1.8.0_92"
Java(TM) SE Runtime Environment (build 1.8.0_92-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.92-b14, mixed mode)

>javac -version
javac 1.8.0_92

> which java
/usr/bin/java
> which javac
/usr/bin/javac

Hope this helps. :)
Neven