To start with, I will notice that in installpath you can always use IzPack way of interpreting environmental variables. For example:

<installpath>${ENV[APPDATA]}\3Dfacto\installers\glassfish</installpath>

Next, ordinary IzPack variables to be used in BAT files.
In your silent configuration files you would like to see something like:

<AutomatedInstallation langpack="eng">
   ...
  <com.izforge.izpack.panels.UserInputPanel id="UNKNOWN (com.izforge.izpack.panels.UserInputPanel)">
    <userInput>
      <entry key="myVar" value="%HOMEDRIVE%\location\file.txt"/>
   ...
</AutomatedInstallation>

Here are some ideas which may help you make it work.

Now, when you use ProcessPanel to launch your bat file, you pass a environmental variable inside a variable. Once you realize it, it is easy to make small trick to make everything work. For example, if in silent installation configuration file (in example above), you provide environmental variable to myVar variable. And then you pass it to the bat file with ProcessPanel in processPanelSpec.xml:

<processing>
  <job name="Install configuratorPortal">
    <executefile name="$INSTALL_PATH/script.bat">
      <env>myVar=$myVar</env>
  ...
</processing>

When ProcessPanel launches that bat file, your myVar will be substituted once. But you need to get it substituted two times! What you may do is to simply add shell call command in front of the expression, where myVar is used. In this case, variable will be substituted twice.
However, it will not work in some cases, for example:

call echo hi> %myVar%

or

call if exist %myVar% echo "hi"

What you can do in this case is to use a wrapper. For instance, if you want to call echo command to substitute variable twice:

call echo hi> %myVar%

Then create a helper parameterDumper.bat:

echo off

:: %1 -- what
:: %2 -- where

call echo %~1>> %~2

Include it into installation and simply call that instead:

call "%INSTALL_PATH%\parameterDumper.bat" "hi" "%myVar%"

Then two call commands will be executed and the parameter will be evaluated twice.

And here comes the power of shell scripts! Some old nasty application runs out of memory every second day? Then what about just restarting it every night? Some third party software results in PermGen errors on high inputs? What about passing data in chunks? There are plenty of things you can do with them! But never use it for long-term solutions!