I found a simple solution, if you can access logs on Agent. There is full set of logs generated in directory %appdata%\Microsoft\SPMigration\Logs. Those are divide in directories by batch as agent scans local storage (usually 10 directories at once). So I just a little changed script written for unzipping downloaded zippped log files from admin center and all is as needed.
Maybe It can help any other guy during scanning or migrating by SPMT tool, which is by the way damn good tool. ;)
Jiri S.