The following does not work for me under PE 3:
[LaunchApps]
%SYSTEMDRIVE%\mydir\application1.exe, -option1 -option2
The winpeshl.log shows only the following command would be launched:
%SYSTEMDRIVE%\mydir\application1.exe -option1
This is therefore only able to launch one option.
To use more than one option with a command, I have had to use quotation marks to process the entire line as one command as if no options. Note there is no comma to separate. It is treated as a full command line:
"%SYSTEMDRIVE%\mydir\application1.exe -option1 -option2"