It’s been almost a year but this is for anyone who might find this useful.
I had a similar situation and unfortunately had to place my modifications in the parent theme.
What I did was to have a folder with files I want to update with the same structure as the parent but with only my modified files then merge it in the parent theme folder.
And before any update, use a tool to check for differences between your version and the update in case your the files you modified have been updated.
If they are, make the necessary updates to your files.
If they aren’t, merge the folder again after the update.
