I'm mostly done now, just have 4 more probes to launch, about 10% more trees, and 80% more arthropods, but I'm finding that arthropod seeding is especially painful. I did not turn up the frequency or size of ore deposits but I'm finding that it's very difficult to find places where seeding works correctly in the near vicinity of my base. Often I think seeding drones should work and then they don't, even when there seems to be everything satisfied. I'm not sure if it's biome-related or if the fumarole distance is higher than I think, but you might consider tweaking some of the settings here to make the seeding drones a little more reliable or easy to work. The easiest solution I can see is to reduce the distance that ore and fumaroles inhibit seeding, because otherwise if people play with higher frequency ore settings it might become extremely painful.

I might try to build rail artillery to get access to more distant spots, but I've already explored everything in range of an artillery 2 and at this point it's a somewhat arbitrary exercise to finish the last bit of seeding now that everything else has been finished.

Also, I see that the boxed recipe for Pylon 3 is labeled Pylon 2 :-)

Overall it was a lot of fun! I would say that the recipe requirements for the end-game gear (1-2M!) is a bit excessive from a balance perspective, but that's just my opinion.

My advice would be to consider the other terraforming tools at your disposal to create the optimal conditions. You can get rid of an entire geothermal or ore deposit with a simple excavation drone. You can create an artificial island for biters, which has the advantage of not only safely containing them, but making it easy to get them in range of lots of fish. An artificial island will be near water and have no ore, so it will be a fertile spot for grass and worms. Unlike some other species, trees you can stack multiple drones in the same area to create a denser forest. The more trees and fish you have the better your odds. Biters don't like being close to too many other biters, so you will probably need more than one area set up for them, but you can easily get 4 or 5 nests in one area. Also, naturally spawned biter nests count, so if you wait long enough it may resolve itself without much intervention. But even if the natural spawns reach 100%, you do need to launch one last drone to get the credit for it.

The end game gear is a bonus for megabase builders. It's completely non-essential to win the game. Think of it the same way as infinite reasearch. Expensive is the point. It gives you something to do with your thousands of science per minute rail bases. If you don't have a megabase, that's fine, pretend that stuff isn't there. It was only added about a week ago, after the original release of the mod, and nothing depends on you having it.

I'll look into the pylon box thing.

The pylon issue is fixed in the latest update.