You can do this with ARJ which you can download from http://arj.sourceforge.net
The trick is to embed command line parameters into the exe which is done by adding a comment which starts with ))
For example, if you create a text file called (for example) options.txt that contains the line
)) -o
and generate your self-extracting exe with the command line
arj A -JE -zoptions.txt TEST.EXE *.*
Then this will automatically overwrite any files (just as if you had specified the -o command line option).