The mod order loads things first-come, first-served and any mods afterwards will overwrite other mods that were loaded before. This creates plenty of issues as sometimes different mods may modify the same objects (events, buildings, origins, etc). It's a tiny bit of a crap shoot especially if you're using a big mod list, but generally mods like universal patches go beneath everything else.
Any patches that modify a given mod will generally go beneath the affected mod (like for example, the Legendary Worlds 4.0 patch would go beneath Legendary Worlds, any mod that alters Star Oath would be under that, like translation patches).

If you wish to create your own compatibility patch for your modlist, that patch would go beneath everything so long as it actually encompassed everything to overwrite everything for the best possible compatibility setup.

It just would take a loooong time because you have to account for Every. Single. Condition. on literally every single object, and NUMEROUS mods alter base game assets, so it's a complete cluster ♥♥♥♥. I wish you a ton of luck man!

EDIT 1: Don't forget universal modifier and resource patches at the bottom of the list, that massively helps things, and if Merger of Rules ever updates, iirc that goes at the bottom too.

Much obliged for the answer! I used to do upwards of 220 mods for the game and after seeing all the nightmare speak of 4.0, figured to head back to basics and make sure nothing on that end is different. One thing I am going to be attempting is compatability patches made via GPT and seeing if they actually function at all after finding out Deep Space Citadels are not playing ball for one example.