Does remapping modifier keys affect special boots? I'm running Catalina 10.15.5.  In the keyboard preferences there is the option to remap modifier keys, which I've done.  My question is, do these remappings apply when using the remapped keys for special booting options like NVRAM reset boots (https://support.apple.com/en-us/HT204063), etc?
No, the operating system isn’t running before boot so modifications to the OS are not in play before it starts.