This is true. And also not true. The Factory is a bit lighter and the Ohlins suspension gives you the "magic carpet ride" meaning it soaks up the little things like only a top shelf suspension can but remains stiff for honest track pace without even adjusting the suspension. And it gets better from there on. I've never worn out a *front* tire at Deal's Gap in a week before but I did this year.

There is some value also in the variable stacks but it's marginal, TBH.
Yes. And this is a better track setup than stock, marginally. The original shock can be re-valved to be 98% as good and both shocks are equally well understood by suspension experts. The TTX is not a "big upgrade" although anyone trying to sell you one will tell you different... the original Factory Ohlins is what they used on WSB/GP bikes in the early 2000s,
far from poor. You won't need to do much to the Factory to get near this level of performance from the suspension but on the other hand you won't save any money getting the Factory as far as this is concerned so if you're looking to build a track bike, it's a crapshoot AFA which direction to go.
The lighter wheels and frame adjustments do make a difference, particularly for a pro rider. Don't discount them, moving to the suggested track settings for the frame geometry and the lightweight wheels will give you more than a second off your laptime on most tracks and let you do things with the bike that no other stock-ish bike can match. The magic of the bike is in its engine tractability and its chassis flexibility (Factory or R, both are great). With another 20hp nobody'd even talk about other bikes, in my opinion.
Why? Aprilia sells a
race ready Supermotard bike and a pile of people buy it and try to use it like a long-term general street bike, and they blow up in 100 hours. Surprise! Anyone who races 4 stroke motocross/motard bikes will tell you that they would kill for 100 hours out of a race motor, but people tried to fit a square peg into a round hole because they had a model that came with mirrors and lights.
However I will agree that the original ones (2006.5?) came to the dealerships with the wrong oil level recommendation as a result of the North American distributor, and that caused engine failures for the early bikes - this was really the NA distributors fault but it will forever remain in people's minds. Sadly.
Go home. You're drunk. And, you're wrong. The very early "R" models, of which virtually none were sold, had an issue with rods that were manufactured to the incorrect spec by a contractor. Almost all of them were never sold to the public and the few that were had their engines replaced.
I have about 10K on my Factory that includes 4 track days, a week at Deal's Gap and a lot of high speed running in an indeterminate place - the only issue that I have had is that the sprocket carrier on the wheel saw the bolts loosen up. Fairly common for that make of wheel and Aprilia has issued a TSB that they should be inspected with every tire change. It's annoying but not something I can't live with.
My Tuono, on the other hand, has been the most reliable bike I have ever owned in 38 (yeah, I'm old) years of owning bikes. It's had seven seasons of pure abuse from me including some track days and a lot of chasing faster bikes down roads without losing ground which requires one to really use the bike to its potential. It's been to Deal's Gap for five weeks of riding. It's been crashed at 80km/h on black ice. The battery is the original, more than seven years old. I could go out and fire it up right now and go for a ride, just like always. It needed a slight valve adjustment at 23500km, just like my GSX-R.
FYI, third party information isn't always accurate.