What can change the nature of the man?
I really see no possibility for this discussion to end - some are stating that they are doing what they are doing because game mechanics are like they are, and some are stating that they just do not like such approach. Everything is fine - everyone has own opinion on that.
Talking about that cheating is no use, it happens and will happen unless it's not encouraged anymore.
Though the problem is still unsolved, yet I'm unsure if it can be solved as easily as some of you are stating ('just remove damned waiting!').
What can be said for sure is that materials from bases need to go. They are simply autoclicker baits and nothing more. Either for example fibers, meat and fruits have to be tended with materials carried from outside of the base, extracted from some dangerous location or they have to be limited and included in the base price.
Like said, risking is the key. Since death has no meaning, players need to risk their gear to get more gear. I heard encounters and farming them will be buffed, if disassembling weapons provides materials for other supplies it might do it. Just need to make sure those encounters can't be abused with insane powerbuilds or other exploits. And that high science doesn't provide more parts, or everyone is forced to make a science-alt.
Encounter-based materials, like junk, wood and healing powder parts could always be guarded by hostile npcs. Also instead of having to look for them by spamming maps, those areas with materials should be easy to find rather than being randomized. This way the rate of gathering is set by how fast you get rid of their guardians. There could be more and less dangerous areas. The more dangerous - the more materials in encounter. Encounters are good because if you die, you lose your gear. If you leave, you get nothing and the next enc has full enemies again. Only abuse is to use a car because it leaves a visible mark on world map. That could be solved by not allowing players to find materials with a car, or allow distresses in those places so that nobody can come there with a car.
It may sound dumb that everything involves fighting npcs like it was diablo. But managing through the hitpoint-reducing strikes of npcs and dealing damage to them in effective manner is one of the best puzzles there is already ingame. If someone comes up with some clever idea for a puzzle that doesn't involve fighting to find materials that'd be great aswell.
Unsafe mines are pretty fine, players themselves set the difficulty there. Sometimes it's non-existing, sometimes overwhelming but there's always a danger present. Problem is that the level of danger is too random compared to the equipment of the miners. Because of this hq mats could be also achieved elsewhere, like from those farmable encounters.
If there comes an occasion where no pks are present in the mine and someone just gets to mine hundreds and hundreds of ores, there could be some npcs spawning and harassing him. The npcs would loot and leave if the player died so that he can't come back and spam the npc to death.
Safe mines could simply have a global limit that restocks random ammount of ores each 20mins. That's the simpliest way, it's like a cooldown but unavoidable. Maybe the ores get depleted occasionally but safe mines are basically like breadline, handing out free stuff.