It was confused but I think I'm understand now. The Migration Tool only can migrate default Joomla components, modules, plugins... but all data related to third party will be lost. It's necessary to have a migration tool for each third party prior using the Joomla Migration Tool otherwise the data from these extensions will not be migrated and will be lost.
I was thinking about the possibility to turn on legacy mode for migration to keep third party working but seems to be impossible.