I wait until after killing Elder, to make my "Main" base, and that's because his altar is the spot i use to build it... by digging out the entire space underneath it.

https://steamcommunity.com/sharedfiles/filedetails/?id=2434837584

https://steamcommunity.com/sharedfiles/filedetails/?id=2434843149

https://steamcommunity.com/sharedfiles/filedetails/?id=2434836833

https://steamcommunity.com/sharedfiles/filedetails/?id=2434836874

https://steamcommunity.com/sharedfiles/filedetails/?id=2432979955

https://steamcommunity.com/sharedfiles/filedetails/?id=2434836940

https://steamcommunity.com/sharedfiles/filedetails/?id=2432979999

https://steamcommunity.com/sharedfiles/filedetails/?id=2434836744

As you may (or may not) notice from these pics, is that: I have only 1 portal in this base, and that's because I built a portal "hub" AT the starting area where the trophies are hung.

I did this because that location is somewhere that needs to be visited numerous times to hang trophies, as well as change powers, AND I didn't want to clutter my main space with a dozen portals... Any time i want to travel to one of my outposts, i simply step through the portal, at my base, which puts me in the hub and from there have all destinations available.

If you can see my minimap, this particular Elder altar is located very near the ocean, which allowed me to set up a docks very close to home, yet just far enough away that it doesn't get raided during regular random raid events. While the altar is close to the ocean, it is also up on a hill, so when I dug out under the altar i was able to dig down maximum dig allowance without hitting water table.

You may also notice some white dots on my minimap and those are copper nodes... Literally have copper right outside my base... can't get much more convenient than that.

The Altar is completely 100% indestructible, and so far, in roughly 450 hours of play, have never had any enemy even come close to reaching the interior of the base, but i must point out that anytime a raid starts happening I go outside to confront the mobs, rather than stay hidden underground.

NO additional walls, moats, spikes or any other form of "defenses" needed... It's completely safe and raid-proof.

As mentioned I have a portal hub located at the start area, so each time i set up a satelite outpost, I place a portal connecting it to that portal hub.
I place new portals any time i reach a new biome or continent or any other important location I may want to go back to.

Each satelite outpost contains a small building which houses smelting facilities and comfort items/bed as well as a bit of storage.... This eliminates long trips trying to transport metals long distances and allows me to simply process any local metals at the appropriate biome.

In swamps I build high up in the indestructible trees, and if you do it right, you can place fires and smelter / coal kiln up in the tree as well so everything is way up out of reach of the poisonous critters below.

Early /mid game, I set up a separate garden area in meadows, to keep my beehives and to grow carrots and turnips, and also happened to place this at an area where an abandoned village has 15 berry bushes that respawn over time. I did this to keep my main base area clear of anything that could get destroyed or attract unwanted attention... Whenever i need foods i just port over to the garden and collect.

For late-game gardening, I set up a fairly elaborate plains biome outpost which sits straddling plains and meadows so I can grow turnips and carrots but also barley and flax, and set up all the necessary processing stations for all the plains resources. The plains outpost is situated right next to the ocean and, with this outpost had to actually surround it with palisades and spikes to keep the bad guys out.

Don't get me wrong, I enjoy building and like the look of various "above-ground" structures (here's an example of one of my early buildings)

https://steamcommunity.com/sharedfiles/filedetails/?id=2425977828

Overall I no longer wanted to be bothered setting up all sorts of trenches/ walls / spikes at my main base and have to constantly be repairing them, so my favorite "go-to" is the indestructible, underground, Elder Altar base.