Devices and connectivity are often changed during LVS comparison due to device filtering, parallel reduction, split gate reduction etc. If you would like to create an ASCII netlist showing the devices and connectivity after these transformations that happen during the LVS comparison phase, you can add the following statement to the rule file before runing the comparison job:
LVS WRITE LAYOUT NETLIST mylayout.net
LVS WRITE SOURCE NETLIST mysource.net
The first statement would cause a file called "mylayout.net" to be created, based on the after transformation connectivity of the layout. The second statement works in a similar way for the source netlist.