So, according to the first post, you can use TSLPatcher to insert files directly into .mod files already existing in modules.
Question is... how? Since I really need that feature for some of my own mods (.git can't be in override and many files that share their name across many modules)
If I remember right, you just need to set your *.mod as install_folder in changes.ini.
For example, we need to add some files to 903Mal.mod and some other files to Override. So [InstallList] part in changes.ini should look like this:
At the end of file we write the list of files which should go to our module and to override:
Files from [install_folder0] section will be addded to ou 903mal.mod, and files from [install_folder1] will be copied to Override.
Of course, you can have more than just one module as install folder, just be sure to give them proper numbers.
I'm not sure if it's possible to configure this with ChangeEdit, 'cause I've never really used it (I configure all my installers by hand with text editor).