I would say the answer is NO, they do not. If you fill out a job application for Tiburon, there is a requirement that you be a gamer, but NOWHERE does it say it is a requirement to be an NFL fan (or any sports fan at all).
These guys are clearly NOT sports or NFL fans other than the incidental exposure they have had working on Madden.
It's as you pointed out with the 49ers: here we have an iconic franchise
whose very icon is the color gold, and yet instead of the gold helmets they have given them tan. And think I know exactly why: They are going off of a two dimensional picture of the logo, using the drop tool to pic up the color, and pasting it on the model. They are NOT looking at actual film to make sure the helmet is right. Why? Because the 49ers were not a concern to them. And why that? Because the only team they were extremely concerned about is the Redskins... because RGIII has sold the most jerseys. Because it's not about getting the NFL right. That's only an incidental concern that only comes up when discussing sales and popularity.
The NFL is a secondary concern to them, I am almost certain. They are all gamers first, and NFL fans only incidentally. That is, and has been, the very thing wrong with Madden all this time. Their priority in their life is video games. The NFL is just a type of video game to them. If the Madden team is ever really going to turn a corner, they need guys who are NFL fans FIRST, and video game fans only incidentally.
When that starts to happen, when instead of guys like Ian Cummings who grew up in Tennessee and hopped on the Titans bandwagon, they have more guys like Kane699, who is a diehard Cowboy fan, that will be the time that Madden starts faithfully representing the NFL.