The way I see it, there could be three things going on: 1) Vanillaware was so done with this game after ten years of development and didn’t want to spend a minute more contributing to their first PC port, 2) they are still ignorant/disbelieving of the recent ascendancy of the PC market despite Sega and Atlus surely pushing otherwise, or 3) someone high up at Vanillaware doesn’t want mods.
We’ve seen the aversion to modding for whatever reason with Japanese developers for a while now. Sometimes they get fiercely protective.