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Its always better to practice migration on a copy of your original schema , so that you can be sure that your application runs smoothly , and any mistake can be corrected :
1- You may not need to backup all your data , only backup what the migration guide says.
2- custom tables - it depends on what you have customized and how much , best bet will be to migrate as per migration guide , and then start the server and look out for errors in server console , then fix them as required.
once your are sure of all changes you need , document and do it on your original data.
migration from 9 to 10 is going to be tricky - multisite - pricing - promotion changes , yeah but it will be very easy from 10 to 10.1
Answer to your question - as your are migration your 9.1 schema - and running scripts on same schema - the same schema and your custom tables will be used for 10.1 , your do not need to export and backup everything , migration scripts are written in such a way to avoid that, else it wont be a migration - it will be a new database installation.
other useful points :
1- Use .bat/.sh files of migration kit , they run scrips in proper order.
2- open the scrips in a text editor and go through it , sometimes important comments are written inside them like which tables to backup before running them.