The throttle body position is opened based on throttle position and demand, not necessarily RPM. Yes, the higher the RPM the more volume of air can go through, but the Whipple is a positive displacement pump, so it builds boost at lower RPM's, but just cannot pump the "volume" which limits it somewhat until you get to the higher RPM. However, the kit is well balanced so you can get 6-7psi of boost at 2k RPMS.
The best way to describe it might be like this. On a stock 7.3L, if you go over an overpass doing say...75MPH and you want to maintain that speed, then the stock engine might downshift to 9th or 8th gear depending on headwind, temp, incline etc. With the Whipple, this does not happen. It stays in 10th and you see the boost gauge get near atmosphere (no boost). The 7.3L holds its gear and RPM, just pulls more power from having more air and fuel available. As soon as you crest, it goes back to -7inHG (or whatever). In driving through the TX Hill Country empty, I put my cruise control on 75 - 80 and it never leaves 10th. Sure on a few of the steeper inclines it pulls 4 - 5psi of boost, but the extra power is just there staying in 10th the entire time. Very similar to how my 6.7L would run.
The Whipple Calibration optimizes the fueling map, AFR, Transmission pressures/shifting to the changes in parameters. I'm fairly certain that the flaring issue is a 10R140 characteristic/build issue with Ford and not necessarily a calibration issue.
Maybe you meant to say "Blower bypass valve " instead of "throttle body". It seems the blower bypass valve would stay open (bypassing) until the manifold vacuum got close enough to atmospheric that boost was needed. Or nearly full throttle. Then there might be a smooth transition where the bypass was only partially open and boost would begin to build. Then under some conditions of full throttle and low enough manifold vacuum (closest to atmospheric) the valve would be fully closed and all intake air would go through the blower and into the engine without bypassing. This could also be used to limit the boost level if boost became high enough to cause a problem, rather than just selecting pulley sizes to limit it. Does it build boost rapidly if you just floor it from an idle, like at a signal? That would be when the manifold vacuum was lowest, or closest to atmospheric, and there would be no need for bypassing.
I've felt that the stock transmission programming downshifted too early on grades, especially when in cruise control. But I have also found that if I lock it into a gear, say 10th, when it wants to downshift, it has a hard time pulling that grade. So, I concluded that Ford got it mostly right, but I don't like it shifting earlier in cruise. Adding boost instead of downshifting would be nice, more like a diesel, and would run at a lower RPM. But of course, the tradeoff is having to run high octane gas, just for the occasional boost conditions. I still want to see some longer term, higher mileage trucks with the blowers and make sure they are not blowing head gaskets. Brian Wolfe has had good luck keeping the engines together under high power output, and I have no doubt the lower end is extremely tough with its forged crank, large bearings and six bolt mains. And the cooling system seems to be completely adequate as I have never seen mine above normal, in hot weather while towing on grades. Very well done! But there is no doubt the bore spacing is very close with absolute minimal gasket surface between the bores. I talked to Brian about this very thing and he agreed. If I put a Whipple on mine, I would also want to keep the original style water pump with the bigger impeller. It seems to me that the only advantage of the smaller pump would be slightly lower parasitic losses. I wonder if the Whipple engine computer programming changes the oil pump flow curve too? It might be a good idea to add more oil to the squirters under boosted load.
I'm still thinking about the Megazilla with its 617 naturally aspirated HP. It also has beefed up internal parts, like forged pistons and, I think, upgraded rods. Not sure on all the differences. It would be fun to compare the HP/torque curves of a Whipple Godzilla and a Megazilla. The Godzilla would probably have higher torque down low, but at some point the Mega probably has higher HP. What is the claimed HP with the Whipple setup?
As far as flaring is concerned, if the flaring stops when you reset or shut off adaptive learning, it tells me the learning is seeking a softer and softer shift and is going too far. Meaning something like too low line pressure. If it does not flare after being reset, it must be going to a default starting setting that is a safe place for it to work at until it learns. Seems to me if we just disable the learning, the problem might not come back. After resetting the learning program, have you noticed the shifts are more abrupt?