There are three ways of telling txt2tags which options and settings to use, and this is the order that they are read and applied:
First txt2tags reads the RC file contents (if any) and apply its configurations on the current source file. Then it scans the source document Config Area for settings and if found, they are applied also, overriding the RC ones in case of conflict. Finally comes the command line options, stronger than the other two.
So, if the document encoding was defined on the three resources, the command line will be the one used.