• The info.note file is being deleted while opening the launcher.
• The setting "close program after launch" (thanks for adding this!) prevents the action of remembering active mods. It only remembers with "close after launch" disabled, or if I close the launcher without launching the game. Looks like it only saves after the "do you want to exit?" prompt.
About the second one, I can just disable that setting, launch the game with various mods and addons variants for testing and then reenable it after finishing, so this one is not really a big deal.
That's all