Nothing confusing here, really. Like most binary file formats AE uses specifc offsets, hash values and check sums for its data. You simply cannot arbitrarily hack around in the file and change the byte lengths. AE files are not meant to be used in this way and there is no tool to that effect. As much as you may not like it, you have to use scripts or XML.
Trying to edit an AEP file using Notepad is going to be as easy as modifying the source code in MS Word or After Effects or editing a JPEG or Photoshop file with a text editor. It's the wrong tool for the job. The right tool to edit an AEP is After Effects.