Migrate module makes the assumption that for each item in your source, you're importing one item into Drupal, and that's baked in pretty deep.
So how do you handle source items where there is body text containing multiple inline images, which should be imported to file entities? For each single source item, ultimately imported as a node, you also have a variable number of images: a one-to-many source to destination relationship.
One way is to simply import the image files at the same time as the nodes whose body text they are in. In the prepareRow() method of your migration class, you effectively do a mini-import, analysing the text, fetching the file data, saving the file locally, and then getting a file ID that you can use to replace into the body text. But doing that, you don't benefit from any of Migrate's helper classes for importing files, nor can you roll these back without writing further code: this isn't a Migration, capital M, it's just an import.