1) MD04/MD16 is for operative planning, but your planned orders are from a simulation, hence they will not be shown to not confuse the people. Talk to your planners to know about the best transaction to show such planned orders (just in case SE16 at table PLAF is not enough for you)
2) All messages are warning messages, however, they prevent you from archiving. Yes this message can go away automatically if other issues are solved. But this is not always the case and cannot be said in general. If it is the last and only error message you have then you may need to debug to know what is causing it.
3) Usually the plant is itself the valuation area. The only other option is if your valuation area is at company code level. Do you really have this error?
4) Of course you can create such program. I would just do SE16 to check if those fields are used in our process at all. If that is the case in general then it might be a good option to have such check report before you start with archiving.
5) if you see this error message then this note is already applied, it is also already in your system if your release is above the mentioned releases.