The difference is this:
You say that "people found a dark magic that duplicated things".
Later you say that "pretending to still have things that were wiped is "declaring that things that are implemented, functional and quantified are wrong"".
However, bugs, lack of implementation and cheats / exploits are not "implemented, functional and quantified", as obviously they are not intended to exist, and therefore even if the entire game mechanics, as designed, were to be considered "the setting", they would not be part of it.
Thus, RPing cheating / exploits as dark magic, even if only referring to it without having done it yourself, is declaring that things that are "implemented, functional and quantified are wrong" (because you would make the exploit a part of the world, which it clearly isn't, thereby unilaterally offsetting the balance of what actually is meant to exist).
Edit:
I even go as far as to assert that explaining a wipe IC-ly is godmoding, because you claim for yourself the right to make a change to each and every character in the world (Because you decide what they have to RP (in this case that a god punished them, or that some godlike alchemist did something to them)).
/Edit
Therefore, there is a huge difference between RPing something that you don't have anymore due to an OOC action like a wipe, and RPing something that you did never have, nor can realistically be assumed to have.
Regarding the issue of RPing fights and RPing paying nonexistant money: this clearly is a problematic thing, and it requires good RPers on both sides to work. It by far is not for everyone. It also means that you have to know, and trust, the other RPer to be a good RPer in the first place, not a godmoder. Therefore, I exercise extreme caution when engaging in any RP, especially if there is bound to be a confrontation of any sort, with an unknown player, until I know what that player's limits are (naturally, I must constantly reevaluate mine).
But the very same thing can happen to you with the combat system: what if you believe that running around, timing weapons and casting magic through houses is how it's supposed to be, but the other thinks that the fighting system automates the entire process so you are not to mess with it? Clearly, the same problems will arise, only that "godmoding" is replaced by "cheating / exploiting". This is especially problematic with magic vs. weapon-based fighters.
Therefore:
If you know the other player is a good RPer, and you have reason to assume that you are one, too: RP fights, for it is more entertaining if it works.
If you are unsure about your or the other player's RP abilities, but know that your and their binary representations are what you both consider reasonable, and also know that your ideas on how to use the combat system are the same, then use the combat system: it will work and have a clear, undisputable result.
IF, however, you cannot guarantee for either, the only option is to refrain from the fight.
Also, as you have observed, discussing and clearing up the situation beforehand (like if dice are to be used, and if yes, how) saves all sides a lot of problems and grief.
BTW, "godmoding" does happily work both ways: you can RP something you have not, which can be godmoding if done wrongly (i.e., you need to have consistently RP'd getting there as well, or at least believably RP'd all aspects of your above average skills, along with resulting weaknesses, for quite a while before actually using them).
But you can also just as easily level up to a completely ridiculous level that is totally inappropriate for all but very few select characters. Even if going by the ingame clock (which runs way too fast to actually use), you can become a master swordsman, second to none, within a few months (ingame time).
Thus, even if you have the skills and stats and money and items, you cannot always RP to have them, and you can still be a godmoder if you do.
I think that both ways, free-form RP on one side, and mechanics-based RP on the other side, have an equally low turnout of good RP. Both can work flawlessly only if the players are good RPers. If the players are not good RPers, then no system I have seen yet can facilitate an enjoyable encounter RPer vs. not so good RPer.
It's merely that free-form RP cannot ever work for not good RPers, while mechanics-based RP can work for non-RP (by shifting the emphasis away from the actual stats and towards who is higher faster, thereby comparing players, not characters).
All in all I think there should, in general, be much less emphasis and willingness to engage in any form of combat, even without dragging in realism.
Edit 2: clarifications
Edit 3: I find it interesting that you mention newbies RPing to have just been born: This isn't even in the settings (if everyone would be born as adult, that would clearly deserve being mentioned). Thus, one must assume that one either just arrived or lived there for a while. Clearly, one needs to glos over tha fact that one doesn't necessarily start with the proper items or status for that. So even here one can'd blindly base everything on the game mechanics, which are, deep down, merely there for OOC reasons (to make things as "fair" as possible for as many players as possible). From a character's POV, the actual "world mechanics" are quite different, and not necessarily fair at all.
Edit 4: There is no single "right or wrong", though: sometimes it may not be feasible to RP having some item that was wiped, while in other cases it may be. Likewise, in many cases it is better to RP a skill you don't have, but by far not in all cases. Common sense, and the feeling of appropriateness, possibly coupled with the feedback of other RPers you interact with, can usually provide the best guidance on a case-by case basis. The maxime of "if in doubt - don't" works even here. I think that most of the time you can ignore the wipe, but in other cases you must find an explanation for it, or just silently cease using something untill you get it back. However, such an explanation is much better something individual, like you losing the item in a betting game (if your character does that), than a "the gods have punished us (even though you might have been the most faithful and perfect disciple of all times)". At the very least, it's not forcing others to follow your explanation for their characters.
