Good question Yeasty

.
The reality is that hops are a black art. We had the head brewer from Little Creatures talk to us once on hops and it was a fascinating talk. He basically said that a lot of the science of hops makes no sense and certainly doesn't match reality and he knows hops well.
For example, he has to produce the same beer over and over again but using different aged hops and different varieties of hops as one year he may not be able to get the hops he used the year or even a few weeks before. In fact, almost every batch of the same recipe he brews uses a different combination of hops. He told us that every variety behaves differently and once you get to know its 'personality' then you can do a lot of different things with even a single hop variety. So, with some batches he may throw hops in the whirlpool that in a previous batch, with a different hop, he may have added 15 minutes before the boil end.
Any software, in this area, can only stop the brewer from making major errors. It's all software really does. Gravity and volume estimates can be quite good but software bitterness and colour estimates will only get you in the ballpark of reality at best.
As to your question, with flavour and aroma hops, what you say is true. There are many different compounds in a hop that create flavour, aroma (and bitterness). The AA% is what we hope will reflect other aspects of the hop (which it won't always) and therefore software uses this number x the weight in scaling. Some brewers however prefer for flavour and aroma additions to work more on weight than AA%.
So, it's a tricky area with no right answer I have ever seen and maybe there isn't one? I suppose the best rule is to try and find flavour and aroma hops that are within the vicinity of the AA% of the hops used in the recipe you are copying.
Because I'm not much of an artist, I usually just do what the numbers tell me to do. If I do have a big discrepancy in AA% of the flavour/aroma hops I have on hand and those called for in the recipe, I might make a bit of a weight adjustment but this is rare. The beer always tastes great so we probably don't need to get too worried.
Other Hop Discrepancies
There are even more discrepancies from brewer to brewer on flavour and aroma hops. For example, some brewers will let their kettle settle for 20 to 30 minutes before they start chilling, other brewers will chill immediately and others will no-chill. Another brewer might even use a hop sock and pull it a little after the end of the boil. So, all these brewers following a recipe that called for a 15 min and 1 minute hop addition may get different beers.
I think the best answer to these questions is for all BIAB brewers to have two side by side rigs and always brew two batches of the same recipe but in two different ways

. Of course, this is totally impractical but doing this is probably the only real way of getting anything more than anectdotal evidence. For now, I suppose we'll have to stick with the anectdotal

.
PP
P.S. In other words, what Bob said

.
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