No offense intended, but so much of what you’ve posted really does feel (to me) like you’re only looking at a very specific, smaller picture.
Crafting would still be gated by owning and maintaining machinery. Are you suggesting that they can have also built themselves a setup with spark and power enough to make their own tools (and maintain any machines they have, obviously)? If you are, then you’re not really saying that changing crafting in this manner would break the game for you, but that it’s already broken and too easy.
Portal networks are freely and easily accessible ‘right now’. Is that still going to be the case come launch? I was under the impression (mistaken or otherwise) that portals were only as easy to maintain as they are because it’s pre-release, there aren’t enough people and they want them in use and being constantly tested.
Your scenario is a ‘best case’ scenario. It assumes no mistakes on the part of the player. It assumes that you will find resources where the atlas says, and not a spot someone else has already been to leaving you to find very little, if anything.
Beyond that, you seem to be of the opinion that if someone technically has the skill and knowledge to do something difficult, or not withing reach of the general playerbase (I consider myself a reasonable gamer, but wouldn’t want to do what you’re suggesting), the game should lock down their ability to do so. At that point, what’s even the point in being good at a game, or carefully planning what you’re going to do if you can never break out of the pre-determined path you have before you?
Time and availability are exactly why it SHOULD work like this. A new player comes to the game a year or two down the line, and sees that they’ve got a massive slog ahead of them to even get close to where other people are. Then they realise that they can’t speed it up or bypass a couple of steps using the economy that has build up in the meantime to catch up at all. They’re not as likely to stay.
Finally, if crafting skills are focused on product quality and material efficiency instead of just ‘unlocks a handful or recipes’, have you considered the possibility that the miner would actually get more by selling his resources and buying more hammers than making their own? This could potentially improve the economy if the focus of crafting skills shifts.