Yeah we discussed this topic
a lot on Discord, many times, as well as a lot in the Beta 11 overhaul thread, but there aren't really any good solutions, so it hasn't changed yet and no other changes are currently slated.
The biggest recent change that did happen was to nerf their capacity, because the base numbers were very high due to being set way back in 2012 for the 7DRL and then simply never being updated despite the rest of the game changing
That alone I think makes it a lot more reasonable. Were you aware of this change? Like energy capacity got nerfed big. Matter capacity currently remains the same, since the numbers were lower anyway and you can't fill it nearly as easily as energy.
Already a bunch of suggestions have been made, but every approach has its drawbacks, and nothing has come out as clearly superior, so unless someone has some great idea that others can't poke a bunch of holes in, it's probably staying the same.
The unique characteristics of the current method are just side effects of the other mechanics combined with wanting to allow people to conveniently store some resources for more flexible builds and situational potential, not really avoidable without also taking away other benefits, or adding other wierdness. (Note we've also already had a time when you could not extract from the ground, or even keep resources stored in inventory, and you had to keep the part attached.)
I will say right off the bat that items working from inventory is not a thing, and will never be a thing. It violates a very fundamental Cogmind design principle and leads to all kinds of other issues.
But anyone feel free to add more proposals for consideration