They're all functionally the same thing with different skins. Just that the GX550 has more commonality with the LC300 GR Sport than the LC250 models have with the LC300. The GX shares the same TTv6 engine and 10AT transmission along with E-KDSS that is the same as the LC300 GR Sport. The front suspension on the GX is also laid out more like the LC300. This is getting a bit into the weeds, but the LC300 front strut attaches with a single sheer post on the front of the lower control arm and is not protected and has the sway bar in front of the front suspension. That is the same with the GX550. The LC250 and Tacoma have the front sway bar located behind the front control arms and higher mounted - the sway bar ends are also above the control arm and protected. The LC250 front coilover lower mount is in a double sheer boxed mount with a through bolt that is protected from the rocks and trail obstacles. The LC250 design is going to be more robust for playing in more technical terrain. The sway bar on the back allows the front end to be shortened and improve the approach angle. The LC300 design is also fine. But it's just not built like you'd design it to go rock crawling as compared to the LC250/Tacoma. 300 is tilted a bit more toward highway use.
Anyway - there's a lot of subtle variation between all of them and they mix and match the parts bin. The new Tacoma has 17 different frames. The MT version has a different rear cross member than the AT version because of the axle hop in the manual. I'd guess there's similar variations between the 300, LX, GX, and LC250 but I don't know all of them. The plus side of all of the options is that the GX550 Overtrail is significantly cheaper than a GR Sport LC300, so you get everything except the front locking diff for a lot less $. And the 4Runner TRD Pro and Overtrail will have even better suspension for off road use probably for even less money.
This is pure speculation, but my guess is the only thing we probably can't get out of the box is an E-KDSS model with adjustable bypass shocks. But I think we'll see most of the tacoma stuff on the next gen 4Runner - like OEM high lift jack points, fox adjustable bypass shocks, bolt on 35s, etc. I suspect the 4Runner will go one increment further toward the specialty off road end of the spectrum than the LC250 like the 4Runner has historically and the new Tacoma does. It's also very possible that the front locker option is saved as a 4Runner option vs going in the LC250. Since it's already an option in the 300 on most trims, that's the only good explanation I can come up with as to why it's not offered in the LC250.