I got this response from another forum:
I don't believe there is a way to alter the defaults other than "hand edit" the xml file. (Sucks I know)
So what I do is save a backup copy of the file and then compare the regen'ed xml with the backup (on Unix use the diff command, for Windows use a tool like WinDiff). That will show you what lines are different. Most of the time you can easily edit one file or the other and you will be back in business.
I wish I knew of a way to change the defaults. I use SSL and a custom kdb and sth file. For me I have to keep changing the references back to my file each time I regen the plugin. This is one area that WebSphere lacks.