Okay, solved it. I changed the desktop file:
StartupWMClass=Code to StartupWMClass=code-url-handler
and added --enable-features=UseOzonePlatform,WaylandWindowDecorations --ozone-platform=wayland to both exec fields (main one and the new window one) to enable wayland. Not sure enabling wayland is necessary, but I changed the file analogously to how vscodium-bin package formatted theirs. I noticed that while I could pin their wayland windows, I could not the stock one. So I created a wayland option for vscode and it worked too.
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