The location and order they are read is very important.
The lisa.properties is read 1st, this is delivered with the larger set of properties provided at the product level. This is installed with the product in the local file system.
The site.properties is read second, this means it can override or replace property key=value pairs. This is only read at the registry level and when workstation, coordinator, simulator, registry, broker, portal connect to the registry they are passed down when the connection is established. This is why you place the database connection information into the site.properties, it is automatically distributed to all other processes on connection.
Then the local.properties is read from the local machine and can override properties previously set or new ones can be set. These are more personal settings at the workstation, coordinator, simulator,, broker, portal level.
When you set properties at command line via -j-d they cannot be overridden by a latter name=value pair, they are special and always maintained.