Unfortunately the manual doesn't describe this either. This is the only discussion on the topic that I managed to find:
"A Mach3 machining system maintains an array of 10,320 numerical parameters. Many of
them have specific uses. The parameter which are associated with fixtures are persistent
over time. Other parameters will be undefined when Mach3 is loaded. The parameters are
preserved when the interpreter is reset. The parameters with meanings defined by Mach3
are given in figure 10.1"
It seems the persistent parameters are the ones you talk about i.e. the ones that get saved in the .xml file. However, what is the interpreter and when is it reset? Also, the list in figure 10.1 doesn't include all the variables that are available in the system nor which ones are persistent and which ones are not.