A bigger problem for me with the permissions we currently have on flathub is that we cannot currently make use of ptrace which our crashlogger uses. Thus no valid crashlog can be produced by flatpak'd Vivaldi in it's default configuration. As a user you could fix this with flatseal or if the crash was reproducible you run it with the following command in a terminal before causing the crash: flatpak run --allow=devel com.vivaldi.Vivaldi
We have a bunch of other small flatpak/flathub specific issues as well, such as when you come to Vivaldi from another browser we cannot detect the other browsers on the system to help you import things like bookmarks, or that Vivaldi cannot set itself as the default browser from within our UI (we can only give you text explainations on how to do it manually). And so on…
This is part of why the flatpak is still not official (despite it being maintained by an employee [me]). Certain things are a indeed a worse experience. However on the flip side it is a trade off many users might want to make for things like additional protection or a more "universal install".