First of all, you shouldn't be running Wireshark as root; to quote one of the README files in the source tree:
WIRESHARK CONTAINS OVER TWO MILLION LINES OF SOURCE CODE. DO NOT RUN THEM AS ROOT.
If you installed the ChmodBPF launch daemon as part of the process of installing Wireshark, that should make the BPF devices accessible to anybody in the access_bpf group (the Wireshark installer should have added you to that group), so that you can capture on the regular interfaces.
Alternatively, you could make the dumpcap program in the Wireshark app bundle set-UID root.
And, in answer to your original question, what happens if, for example, you quit TextEdit and then do
sudo /Applications/TextEdit.app/Contents/MacOS/TextEdit
Does that running-as-root instance of TextEdit use the alternative keyboard layout? If so, then the answer is "programs run with sudo will use the default layout"; if not, the answer may be "programs using Qt run with sudo will use the default layout" (in which case Google Earth might have the same issue).
