...I think the defense has the better argument. I have used software tools (both third party and ones I have developed personally) to do source code comparisons and analysis, but they only serve to point me to likely areas of investigation; I have never directly reported and relied upon the output from one of my custom tools in my expert reports.
A key aspect of expert testimony is that your analysis should, in theory, be repeatable by any other qualified expert using the same methodology (which needs to be spelled out in your report). If Perlin is relying directly upon his custom program for his conclusions, he needs to thoroughly expose his methodology -- which, in effect, means either allowing his source code to be reviewed or producing a detailed summary of his methodology that would allow someone else to reproduce it. Trying to claim trade secret status (which is what he's doing, in effect) for a expert methodology is an oxymoron.