While I don't necessarily disagree with the broader premise of your argument, a couple things stand out.
Very few strikers are elite in terms of their overall game at the age of 21 (approaching 22). Van Nistelrooy wasn't elite at 21, Vieri wasn't, neither was Inzaghi, nor Villa or Drogba or Eto'o, and so forth. We look at the likes of Lewandowski now as a veritable prototype for a modern #9, but at the age of 21, he too was a work in progress and was a couple notches below what he eventually became in 2012 and beyond (both in terms of creativity and goalscoring). Infact a lot of supporters were opposed to buying him even in 2012 at the age of 24 (we were linked with both him and Kagawa in the summer) because Van Persie was deemed a better, more proven and accomplished striker overall, something that seems a bit misguided in hindsight with Lewandowski's elevation is status. This isn't to say Kane will replicate the level of improvement and consistent productivity that Lewandowski did, or some of the other modern striking greats did, but at the same time he isn't exactly technically stunted to be honest, is still a rather young player and will progress as he gains more experience, and confidence, and learns the subtler nuances of the position. We aren't going to buy for what he's already done, but more with an eye for what he could do in the future.
The Rooney example isn't supposed to be a rule of thumb either. Someone like Rooney has arguably been superseded by Costa, who was terrible at the age Kane is right now. Another like Shevchenko delivered on the initial promise at Kiev and Milan. Moral of the story - different players progress at different rates, some are more naturally gifted but are eventually overtaken by their more determined counterparts, so it's disingenuous to arbitrarily bring up Cesc or Rooney. You're right though, from a strictly objective standpoint - Kane doesn't have a great overall body of work to extrapolate a reasoned judgement. And he might never become an elite striker for all we know, but he fits Van Gaal's requirements really well. What if he develops into an elite type forward in 2-3 years' time, and we pass up on the opportunity to sign him, while he's scoring 30+ goals each season for a rival ? Sometimes you just need to grow a pair, trust your gut, and make a semi-educated guess (which might be what Van Gaal is doing right now if the media reports are to be believed). It might backfire, but United has been served well by trusting developing players and have always been one of the more progressive clubs in terms of acquiring raw young talent, and polishing them into the final product rather than buying a glut of players in their prime off the shelf. Maybe it's an archaic notion and it could be argued we've had a lot of flops in recent seasons, but the policy shouldn't be forsaken in its entirety, watching younger players grow really is part of the charm of the club, and something that's embedded in its DNA.
As for the fee - it is largely based on his projection, not just Kane's current level as a player. So that, alongwith the premium on homegrown players and Levy factor means that the figure is going to be naturally inflated. And it shouldn't ideally concern normal fans like us. If the owners and Woodward are willing to pay that figure, does it really matter ? We have more than nough money going around to fill other holes in the squad even if he pay the touted transfer fee for Kane.