Quercus is a Java implementation of PHP 5 developed by Caucho and implemented inside of their application server called "Resin". The most significant difference between Quercus and the Runtime Converter is that Quercus is a way for you to run PHP on the JVM, rather than a way for you to convert your PHP source code into Java. It is offers a way for you to call Java from PHP, but it is not a way to convert your site from PHP into Java.
The Runtime Converter not only compiles to Java, but provides you with a Java project source that you can edit.
Another advantage that the Runtime Converter has is that using JNI it has access to the real PHP function implementations. Quercus has implemented the majority of PHP functions, but there are a significant number of unimplemented optional parameters and certain to be a number of additional implementation differences. By comparison, we can rely on the implementations we have, as they are the exact implementions used by php (written in C).
There is one advantage that that Quercus has that can be useful to the Runtime Converter. The fact that it is written in Java means that its functions have a lower overhead than the JNI functions that we use. In theory, an enterprise client could purchase a license from Quercus and then pay us to implement, intergrate, and test some or all of the Quercus functions into the Java runtime and converter. That is, if they wanted to convert to Java rather than Swift or C# which have a much lower or even negligible overhead of calling into the PHP runtime.