The reason for that is clear: this system is arbitrary with regard to real-life salaries and is based on principles that are sound theoretically but do not mirror real-life salaries precisely. It's an equal-opportunity deal in that regard; everyone is subject to the same principles.
There are several factors in real life salaries that are simply not reproducible here. Frontloading and backloading, guaranteed and un-guaranteed money--that stuff can't be worked into this system without lots of hassle.
And keep in mind: the principles that govern the contracts in the OF are really designed to get things to function properly *after* year one.
Take a guy like Revis, for example. He's in the latter portion of his first deal, which often under-values guys (Chris Johnson too). In the game he's paid like he will be under his second contract, but in the OF we have to value him as-is.
Now, next season, you will be able to draft a guy and pay him below market value for 3-4 years if he progresses nicely. This year we've scaled it to where the big money will come in that second contract phase between 26-29 or thereabouts, with younger and older players generally costing a bit less. Thus, going forward it will be possible to have young talent without paying through the nose.
But in order to get that system right for the future, we have to begin rough in the first year because everything is calibrated toward the values that will obtain in the OF, not those that obtain outside it.
Bayern was upset about BAL last year, but it just is what it is and you gotta get with it and make some tough choices. SF is in that same spot this year. IRL they're fine cap wise; in Madden I have to make some really hard calls this off-season or get really creative financially.
If you have a better idea for how to do the cap, there was a lengthy period in the off-season for bringing those forward, but nobody really did that with any precision or in a really compelling way (I argued for real dollars but didn't get that to stick).