There is a pretense that the policy of the club is in some way consistently applied, but as I hope to highlight in this post, that is not necessarily the case.
To use the example of 19 year old Phil Jones (although there are any number of others), does anyone really believe that he was signed from Blackburn on a contract worth just £20k per week? Of course, Jones had appeared in Blackburn's first team for an entire season which is why several clubs were prepared to pay £16m for his signature.
But it's worth noting that Paul Pogba will never have that opportunity because he was prepared to leave his homeland and the club that developed him at 16 years of age in order to pursue a career at one of the biggest clubs in the world. Should Pogba go on to become a first team regular at Manchester United, the money saved in transfer fee alone (on the basis that it would have been similar to that of Jones) would pay his wages for roughly half of his eventual career at the club. Which is not bad considering that the club played only a secondary role in his development.
The point here is not that the clubs policy is unreasonable -- at least, not as a general principle. But we should not pretend that it is internally consistent or that it is the most altruistic expression of fairness and equality that has ever been devised. It is quite clearly a policy that is designed to benefit Manchester United first and foremost, both in sporting and financial terms. So, it should be unsurprising that such a general policy is not necessarily applicable in all circumstances.
And we can't have it all ways. If we wish to attract players at 16 years of age, knowing full well that it will be much harder for them to 'earn' the financial rewards of a first team squad member, while at the same time signing 18-19 year olds for tens of millions and offering them first team contracts on the basis of appearances with a team where it is much easier showacase their talent on the appropriate stage, we should expect these inconsistencies to be pointed out and possibly even for them to influence player behavior.
There are also two further problems with this policy. It may appear perfectly reasonable that a player should have to earn a contract worthy of a first team squad member, but there will likely always be a point at which an individual players contribution surpasses the market value of their current contract. In other words, it is inevitable that when a young player signs a multi-year contract the natural process of development and maturity -- should they develop at the expected rate -- will mean that the value of their talent and contribution exceeds their current remuneration at some point during that contract.
Now, to be fair, this is precisely why the club is willing to renegotiate so early in to a new contract, but that doesn't change the fact that one of the parties will lose out for an admittedly limited period of time, and that the clubs current policy -- whether by accident or design -- ensures that it is usually the player. That is, unless it is a player bought for a large fee, in which case the club is often prepared to pay a salary that far exceeds the players present contribution to Manchester United, and in the knowledge that it may take several years before that contribution respresents value for money.
Which leads me on to the second point of contention; that the policy inherently implies that the club does not believe/trust that any individual within the academy structure is likely to become a first team regular. No matter how long a player has been at the club, and no matter how highly rated they are, the club are not willing to place their trust in any individual player -- financially, at least -- until they have 'earned' it in the first team.
In one sense that is perfectly logical as the 'academy' structure and therefore the policy applies to groups and not individuals (and the clubs actions with respect to one individual can affect the group), but the club is nevertheless dealing with individuals, and the example of Phil Jones and many others shows that there is a disconnect between players that have been with the club for a period of time and those that are bought from elsewhere.