This is a valid (and with the current code, sometimes necessary) workaround for certain things the current UI doesn’t give you a direct or easy way to do.
As long as it remains a valid ASS file, we don’t really care who created it or how. But I would recommend that if you are going to do this, you save your project and exit kdenlive, then restart it again after your manual editing.
The actual handling is a little tricky, while kdenlive is running there are two copies of the .ass - there’s the project files which get updated when you save, and loaded when you open a project. But there’s also a ‘working’ copy which contains your unsaved changes and is what gets rendered during playback (and restored from during crash recovery). So there is some risk of confusion/corruption/loss of work if you edit it manually while kdenlive is using it.
My list of irks with the current subtitle code are here: 24.12.0 subtitle editing and I’m working on fixing them, so feel free to follow up there with any of your own you’d like addressed too.