Hello gorkovchuk,
It would be helpful, if you could share the complete processing log from the beginning of the task from the version 2.1, that contains the task starting parameters. Also PDF report from the same project processed in 2.0.4 version.
And please provide the screenshot of Align Photos dialog with the settings used from the both versions, as there might be some confusion in this phrase: "16000/64000 key/tie point limit per Mpix".