Hi Ali,
I'm glad that you like it.
Changing Chrome version is a bit of complicated process, you will have to wait for an official phpdesktop release. You could do it yourself if you have C++ knowledge. But I won't provide support in that matter, you would be on your own in doing so.
You can create a single executable file for distribution with the help of Inno Setup installer. That is how most of the software is distributed. See the KnowledgeBase wiki page for links.
If you use google you might find tools that provide a way to create a self-extracting executable that extracts its content on the fly and can run program from some temporary directory. Of course the time needed for extracting would delay launching app a bit.
There is an issue in the tracker to allow embedding static resources (js/html/images) in the phpdesktop executable. There are no plans on embedding php scripts in the executable. You can use php encoders to hide your php sources.
Best regards,
Czarek