There does not seem to be an option in MESSUI to turn ON/OFF the following:
#
# CORE CONFIGURATION OPTIONS
#
readconfig 1
writeconfig 1

ShadowMyst should make sure that these options are on in the .ini file for the desired emulation. Then ramsize can be set from the main MESSUI window for each desired emulation and it should be remembered. It is for the systems I want to use.