What happens to the body when agent appears?

OK, so agents need their batteries' avatars to spawn to places (such a stupid design, why would they need this?).

However, what happens to the human, whose avatar is taken over? Does their physical body suddenly look like the agent? (Your mind makes it real..)

When Neo blows up Agent Smith, what happens to the human that inhabited that body? Mind makes it real, so does their physical body explode suddenly?

How about when the agent 'inhabits' their body, what happens to the physical body, do they die, or fall into coma? Does the battery stop working and does a spider droid come to inspect the body in the pod?

I mean, if they can have their batteries invaded like that, WITHOUT the people 'rejecting the program' and this becoming a 'whole crops were lost'-type problem, then why couldn't they simply invade ALL avatars with agent programs? It's just software, so it doesn't 'cost' anything extra, energywise anyway (maybe slight increase in CPU power, but then again, agents would not need such 'realistic reality', so they could massively cut down on the detail to make it look like early 1990s filled vector games with no textures or complex polygons or detail of any kind)..

I have so many questions about this whole 'agents take over an avatar' - what happens, if an agent doesn't murder that avatar (I still have hard time believing someone's mind would make a death real, when an agent is inhabiting that avatar, so how can it even feel like THEIR death, when it's just the 'agent' that dies? So how does your mind know to kill you, when from its perspective, it's either in some kind of coma, pause mode, and in any case, is basically possessed by a program?)..

I have so manu questions about how it all works, and this movie doesn't answer any of them. Can they 'wake up' from the coma if the agent jumps to another avatar? I mean, one moment, they are in Hawaii, having a great holiday, then suddenly they wake up in New york 12 years later.

What happens to their 'avatar' physically? Do they 'save' the physical form and condition they were in before the agent took over their avatar, or can they gain weight, age, lose hair, etc. while the agent is in control, or what happens? Their physical body ages anyway, so now it's incongruent with the avatar, although it's supposed to look the same.

I have so many questions like these, I can't even write them all down here, but could someone explain how all of this is supposed to work? I bet the Watchowski _B_R_O_T_H_E_R_S_ did not care to even think the details this far anyway.

I just see that none of it makes any sense. How far does this 'your mind makes it real'-type non-explanation go? I mean, if you are run over by a train but the agent is inhabiting your body while it happens, does your physical body get MANGLED like it would by a train?

If someone blows up the avatar, as Neo does to Smith in the end, does the mind of the possessed individual make the physical body in the pod explode, even though the mind is NOT AWARE of such physical body..?

How can the mind 'make it real', if the mind is not even AWARE there is a 'real physical body'?

So many questions... so many questions.. the horror.. the horror..