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But you can still lose the resources in your storage through node sieges, so there's really no differentiation there. Which is why I think that as soon as you gather/pick up some resource - it's yours until taken or traded away.
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I think it's about the value of time more so than the value of the resources themselves. Or, well, at least that's how I see it. If I spent an hour or two farming some juicy location deep in a dungeon (be it mobs or rare gatherables there) and then I get PKed and lose a big chunk of the resources, my immediate reaction would be "a shit I wasted a ton of time". And while I'm a person who would immediately go and try fuck that PKer up, I'd assume most (or at least majority) of true greens would just feel bad about their, already limited, playtime being wasted by another player.
And with travel times being longer than just "tp here then tp there", if you tell all greens to just run to the city every time they pick up an item - they'll tell you "you're crazy"

And that's not even considering that leaving your location usually means giving it up to someone else, so even if you do go to the city often you'll be losing out on more of the same resource (especially if it's rare and only has a few limited spawn points). Flagging up and fighting back removes that part of the equation and obviously lets you lose less stuff if you die, which is why I like this mechanic.
But I'm sure you've seen several threads where people complained about being constantly killed or having only 10 minutes a day to play the game or anything along those lines (or just not wanting to pvp if they're not in the mood like Dygz does). To those people the thought of "protect your spot and you'll get to enjoy the game more" seems to be as alien as "I want everything to be instanced" for me. And I feel like giving them some potential insurance for the time spent, while also letting the PKers kill a few more people a day, would go a long way. Though those PKers would still have to be caught first, so it's not a 100% insurance.