I think this is a normal (and unhealthy) consequence of the JS browser APIs keeping expandong. A sort of Greenspuns Tenth Rule Of Programming that happened on the web platform.
I am not sure there is a cure. Every successful platform would have been bound to eventually become that.
AWS has this thing that allows you to connect to an virtual machine from the web console, giving you browser based terminal. Very convenient and nifty. Except using ^W to delete word is so hardwired in my muscle memory that I ended up accidentally closing the tab (and losing state) endless times... I don't think its solvable problem
That being said, same issue happens, albeit to a lesser degree, with desktop apps where occasionally the DE/WM shortcuts conflict with some applications shortcuts.
In Firefox you can enable the ui.key.textcontrol.prefer_native_key_bindings_over_builtin_shortcut_key_definitions setting, but I think you also need to enable Emacs keys in Gtk.
With this I'm able to use Ctrl+w normally in the Gitpod terminal, so this might work for the one in AWS as well.
My personal annoyance is when they hijack cmd-f to implement custom search functionality. Especially (but not only) when they fail to handle cmd-e and even more especially cmd-g.
I even understand why in some cases it’s necessary to provide custom search. For example to implement search over lazy loaded content which hasn’t yet loaded. But it never works as expected, even when it’s done well.
E.g. Outlook Web hijacks CMD+R on my Macbook, of all things.
Wouldn't want to miss CTRL/CMD+K in some web apps though.