Recent versions of Sharegate have the option to Auto-Assign Site Collection Administrator in General Settings, which allows Sharegate to automatically assign you as a Site Collection Administrator when running Site Collection or OneDrive for Business operations.
To revert this selection, you need to use Sharegate Management.
Note: the below steps use OneDrive, but you can apply the same steps to a site collection.
Select Reporting, and click New Report
Select for OneDrive for Business
Click Continue without Saving
Target OneDrive for Business
Select all results using the top left check box.
Click Edit selected items
Use the drop down to select Remove Administrator
Select yourself or any other applicable user who you are removing administrative rights from.
You will now see the results page.