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Can you post some screenshots to show the difference?

just create a project in the TC3 ... setup all stuff as DC, SDOs PDOs, task cycle, names of everything ... everything will be written in the .xml of master export ... there it will be right stuff and there will be probably nothing to customize ... 

download the tool ... launch them .. write "complete" or "c" .. then drag and drop .xml export and everything what is needed to have in the .xml file will be created in the new ethercat-conf.xml automaticly .. then just connect everything in the .hal file

AX5xxx is SoE .. you will have to create custom hal driver for them probably... I do not have experiences with them at all

I do not know what which "ax5106.xml/ax5203.xml" you mean..

motor you need to tune in the beckhoff drive manager which is part of the TC3 ... it motor is in the catalogue, no extra tunnig is necessary