As of 8.0.3, local and instance variables should work in Prompt For User Input and Custom HTML Input windows.
Also, you can now access them from scripts by using the KMINSTANCE environment variable as a key to which set of variables.
set inst to system attribute "KMINSTANCE"
tell application "Keyboard Maestro Engine"
set v to getvariable "LocalVar" instance inst
setvariable "LocalOut" instance inst to "FromAS"
end tell
v