The issue is that you have to continue "fixing" lots of individual utilities. In addition to your file manager and `ls`, what about tools like `fd`/`rg`/`ag` (requires adding `snap` to `~/.ignore` or `~/.gitignore`), `fzf` navigation in the terminal (may require updating `FZF_DEFAULT_COMMAND`), "open file" and "save file" dialogs in non-GNOME apps (like Zotero), and so on. The `snap` directory keeps popping up in new places, and discovering all the different ways to hide a non-dot-file is exhausting. In contrast, adding that initial dot to the `snap` directory would avoid the problem entirely.
I have still been using `snap` for the past year, and have mostly been happy with it. It works well for apps like `spotify` and `zotero`, it's a better solution than `ppa` for third-party software, and I like that it tries to introduce a permission model. But not following the dotfile convention is annoying, and not prioritizing a search-and-replace of `~/snap` to e.g. `~/.snap` in the code after four years is strange when this is their most upvoted bug.
