There is no need to scale anything, never. Now, this is not the issue you had, where it leaned out up top that you solved scaling (but something else was needed), think the tuning like modeling, you are developing a model of the engine and the system is already designed to work on real engineering units, that reflect actual physics of what is going on with the engine.
While tuning you have a set of variables, so you choose to establish the ones that you actually know for sure as fixed and leave the less unknowns as possible that are those that you play with. You know your engine displacement, you have a complete set of injector characterization data, you use that, fixed, because it is true. What you don't have is data about your intake tract and that is why we chose to tune via MAF, because we chose to leave that as our variable (specially in a case like the OP) as it is the biggest unknown. This way you relate everything and end with a working model.
Now, why was scaling introduced? mainly because some older PCMs had binary limitations on some of the data it had to manage for mods that needed bigger numbers (later a nice trick was introduced to avoid this in certain cases), so you needed a number of airmass/flow that the PCM had no space to deal with. Solution: make an scaled model of the same engine, by a percentage, the same percentage you needed to add so you would have range to work.
Typical cars that suffered this were terminators, PCM had limitations but engines were capable of moving huge amounts of air with a few mods. You reached the limit easily so the trick was to scale everything, this is were the MAFia comes to the picture. Let's say you had a healthy termi with pulleys and mods. You used the same MAF sensor that came stock, with a few mods you find you reach the 5v-64#/min of the calibration, what to do? get a MAFia, and do the recipe they suggest, why? because you reached the PCM limit and need to scale, let's see you scale it by say, an hypothetic half? in essence, 2.5 V would be the same past 64#/min, but in the tune it would read half that value: 27#/min, but the injector data was halved, as displacement as other stuff (that needs to be scaled to and they don't say it), it all has changed but all, in reality, stays the same.
THIS is why the diablosport page says that.
Now, with out powerpc cars, I have not found a binary limitation in them, so you can use ANY kg/hr-#/min value you want, so there is no actual need of scaling, the kind of need the older PCMs had.
What you use a MAFia for? a DC-DC voltage converter, develop your new MAF table and be done. Use the correct data everywhere else. Load will be just right.
In the OP's case, let's say he had a 4" housing for the MAF before, at idle it probably read let's say 20x counts/1V and that translated to 1Kg/hr worth of airmass/flow. Now you move it to a 3" pipe, the same sensor and using the same tune file, it would idle at say, 30x counts/1.5V but right there, airmass/flow in our original MAF transfer has 2Kg/hr, so car will get way to rich.
Then, if you had access to the tune file, and you mod the table to reflect 1Kg/
[email protected] then the car would idle exactly as it did before, load will be the exact same. IT DOES NOT matter that the voltage was higher than before, at all.
And now, you get a MAFia, but use the previous tune, without modifications. And with the MAFia, you make it work so actual 1.5V at the MAF will be converted to 1V, the previous tune will work as it has always worked AND load will be correct. so, there is absolutely no need to do anything with anything else in the tune when using the MAFia.
The problem is that a lot of tooners (not you Bruce, I am talking about people that present themselves as such and charge for their toons) do not understand how the system works and takes every info they read as valid. I have seen some people doing this (scaling because of a MAFia) and ending with horrible mannered cars. Diablo should correct that and be clear on what are they suggesting and when this should be applied but I would not wait for that, if they haven't updated their tuning software to something that would loosely look like to a century XXI application, would not wait for them to do it.
Sorry for the long post and hope I was clear enough.