The problem is that statement is 'progression should be balanced without skills' and the only way you can do that is by not having skills affect progression.
I do get what you're trying to say but it doesn't work that way. You made a choice not skilling into harvesting and that has an effect. That's your choice. T2 tools (and probably weapons too) are better if you skill into them especially for the roles that play in (for tools harvesting time). That's how the game is balanced because the devs with the data looked at, and figured out that was best for the overall whole system.
I do get what you're trying to say but it doesn't work that way. You made a choice not skilling into harvesting and that has an effect. That's your choice. T2 tools (and probably weapons too) are better if you skill into them especially for the roles that play in (for tools harvesting time). That's how the game is balanced because the devs with the data looked at, and figured out that was best for the overall whole system.