Well, I've gotten my eyes on the RAW. Very weird.
Looking at the tables on p. 11, a botch will create a regio with a mundane level (aura 0) and a top level of the ovreall aura score - only two levels, per page 13, are created this weay. The entire area in which the aura is located becomes a regio; this isn't like in your scenario, where only a part of the aura becomes a regio.
The botch may also result in a new level within an existing regio, in which case the wording on page 13 implies to me that the regio levels need not be in order, but that the top-level must be the highest (the aura score) and there can be at most (aura score+1) levels, including the mundane level (aura 0).
Once a regio forms in this way, increases to the aura score will increase the top-level, so won't create a situation wherein the lowest level (aura 0) will acquire an aura. A botch may result in an additional regio level, but that too won't change the already-existing lower level.
So my conclusion is that the RAW says that the aura in the lowest level is always mundane - aura 0. The rules presented in RoPM do not result in the creation of a situation wherein the aura in the mundane world is anything other than zero; the aura strength inside the regio's first level can vary.
The only possible exception seems to be a a magical event or accident, which is not fully covered by the rules in RoPM. Botches are, though, and seem to be what is intended - and so won't be a way out, too.
All of this is very weird, as regiones are typically found within auras, not within mundane (aura 0) areas. I think it's best to just ignore that aspect of the rules. Let the regio form in a part of the aura, with the lowest level (the aura in the world) kept as-is and the new regio level initially at the same level. The top-level of the regio would then increase with aura increases, I suppose, a per the usual rules.
Since you'd be houseruling in that case, I suggest you might want to consider other options - so the aura inside might be lower than that outside, and so on.
While I like the idea of the aura change rules, I don't really like their execution. This is an example - magic regios arise instead of magical auras, not in addition to them. Another is that things botches always create regios - there surely should be other effects. Another is that I don't think impinging and competing auras are done too well. There is no option, for example, for a spirit to form all alliance with a Faerie power to maintain the aura, as per GotF. There is little way for a weak aura to grow within or from outside a strong one. There is little way for an aura to expand geographically - only by a few yard per year.
Another way to make regios is with a spirit power, of course (page 105), and this does create a regio within an aura, rather than replacing the aura.