"You allow everyone to have all the skills or all the resources, you limit other parts of sandbox, like trade and exploring, even a sense of community."

That is exactly the opposite, if you let people to farm certain spots you limit the exploring and then trading which explorers could of found and traded in for something else.

"Large projects if they are easy to do, or done in a second or 2, limit other parts of the sandbox MMO. Like where you get a group of people together to accomplish a goal."

Large projects like building a city is imposible by homestead because of a small land, that is why who want to build large city they group together to accomplish that goal or gather a group of people to kill bears or tough revs.
So there are things that needs grouping, solo players need something to do as well, at the moment solo players are limited, in a sence of progression.