Many MODS interact with custom profile fields. When upgrading from a mod to an extension, these extensions will want to manipulate the profile field data.
The sql_prepare_column_data function, accessible to the migration tools, currently doesn't allow for column data that assigns the default value of a column to NULL. This is necessary because the save_profile_field in includes\acp\acp_profile.php does allow for this (and uses it by default).
In other words: it is currently impossible to insert/manipulate profile fields data to the same degree as in acp_profile.php, because the perform_schema_changes cannot be used to create columns the correct way (with default == NULL).