Unfortunately, we don't know what exactly different SQLite database tools can do with database file. But you should pay attention to the VACUUM
SQLite command.
The VACUUM
command cleans the main database by copying its contents to a temporary database file and reloading the original database file from the copy. This eliminates free pages, aligns table data to be contiguous, and otherwise cleans up the database file structure. See more on documentation.
So, as a workaround solution, you can apply this command to your database, when you finished to work with it in any specific tool.