No, they didn't essentially sign 6 year contracts. They signed 4 year extensions. The fact that signing bonus can be paid before the 4 year extension kicks in doesn't change that. A signing bonus is a money paid in exchange signing the extension deal, not in exchange for playing years they are already under contract to play.
By your thinking, if I sign a 12 month lease on some office space, but pay the first and last month's rent 2 months in advance in order to lock in my spot, that makes the lease a 14 month lease. That's wrong because all I'm getting is use of the office for 12 months. The fact that I make payments over 14 months doesn't change the fact that what I am paying for and what I am receiving is use of the office space for 12 months.
That analogy is really poor.
If what Wentz signed was a true 4 year extension tacked on behind the last two years on his rookie deal, he would have played under the terms of that rookie deal. But he didn't. The 4th and 5th years of his rookie deal were restructured. You can pretend that didn't happen, but in fact, it did. When the Eagles picked up his 5th year option in April of 2019, that locked them into owing/guaranteeing him $22MM in 2020. His cap hit in 2020 would have been that $22MM plus whatever residual bonus money was prorated. But when he then signed his "extension" in June 2019, his 4th and 5th years on his rookie deal were re-worked. His cap hit, for example, in 2020 went from over $22MM to 18.5MM.
Further, the majority of his bonus money wasn't paid when he signed the extension. He got a $16MM signing bonus, but then the way the Eagles worked the contract, they then created an option bonus for 2020 for $30MM that he was paid this year. So what they have created was a $16MM signing bonus that they spread out from 2019-2023 and then an option bonus of $30MM paid this year that spread out from 2020-2024. And the cash payments confirm this. In 2019, when he signed the extension, he pocketed $17MM in cash (base salary of $720M - from his rookie deal plus the $16MM signing bonus). Then in 2020, he will pocket close to $40MM ($30MM option bonus, a $8MM option bonus and his base salary of $1.4MM). If he was simply playing out his rookie contract and then had the extension kick in, his base salary in 2020 would have been around $22MM, not $1.4MM.
So when you know the details of the extension, it's clearly not a standard extension simply tacked on after the remaining two years of his rookie deal. With the extension, they made material changes to the last two years of his rookie deal basically creating a new 6 year contract.