Thanks for your interest in iInstall and the nice word about it ?
To answer your questions:
There will be an option to build packages using command line parameters in a future version.
To build EXE files will not be a part of iInstall Reborn. This is possible by use of other tools. One such tools is Launch4j that will build one EXE file containing the JAR file build by iInstall and it could also include the Java RE if your customers does not have Java installed.
For further information about Launch4j, please have a look here: https://sourceforge.net/projects/launch4j/