First, for already closed source programs the obfuscation results don't make a difference at all. They remain just as obscure before as they are now. (Unless you routinely try to de-compile all closed source programs?)

The obfuscation result in the submitted article really only makes a difference to open source programs.

But: thanks to advances in mathematics and cryptography, a vendor can prove to you that their program does what it's supposed to, without having to reveal the source code or anything else about the program.