When using Skip N hours on a new game start, all research which has an event-based trigger are researched by default. This includes super late-game research like the cryogenic and electromagnetic research. These technologies have a research_trigger instead of ingredients. The force_util.research_enabled_techs_by_items function researches them because the research_unit_ingredients is empty and it falls through to researching them.

Can you just run this to solve:

/c for _, tech in pairs(game.player.force.technologies) do
tech.researched=false end

But i fear something might get broken...

I'm going to fix it today.

Good catch from theit8514.

It should work properly now in theory.
Please, confirm.