After reading and going back and forth with a few devs, here is what I have found.
#1, when you flash the files, the system still shows the Baseband versioin is on N900AUCUBMI9 (this is good because it was not this was originally the case)
#2 Flashing root this way is different than the original method and does not trip the Knox Flash Counter. (Originally I thought the knox eFuse and the flash counter were different, but they are not) So your flash counter will still show 0x0. This is really good because once an eFuse is "blown" is cannot normally be reset.
#3 Rooting will show a custom system status and unlock logo that AT&T is told to look for. But...
#4. The custom system can be reset/faked/removed by installing Xposed Framework with Wanam Xposed and enabling Security hacks > Fake system status.
I still have issues with #4, this may or may not be true but I want to point it out.
History, I don't remember which phone (I think it was my Atrix), but when the OTA update came out, as it was installing, it did an MD5 file check as it did the install (including the framework and system files). If the MD5 failed, the update failed at that point and bricked the phone.
To install Xposed, it replaces a file in the /system/bin folder (this is a system file), this is important as it modifies the system files it make it work; and even if you remove root and Xposed, your system is not 100% back to normal. Plus to get rid of the custom system and unlocked lock, you have to install the Wanam Xposed apo from the play store. If you flash back to stock (which the AT&T warranty center does and what AT&T does when you send in your phone for repair), does the fake system status get undone and you are busted, or does this stay?... I'm waiting on this answer
More issues with this that will be unknown until an update comes out: Since AT&T has not released any OTA updates yet, the devs do not know how the update will work when in installs. There is a chance, that either you will not be able to install the update OR if it tries (most likely with AT&T), it may find/see the modified files and fail, bricking the device.
Ok so what does this mean? Well it means if you do root, you may not be able to update to when it comes out and have to wait until the devs modify the update to work with a rooted phone. It also means even with the tricks to make your phone look like it is stock, it may not be the case... I'll repost as soon as I hear on this part
UPDATE UPDATE UPDATE UPDATE UPDATE UPDATE UPDATE
Well I can't get an official answer but everything I reading, as soon as you flash a rom (which we can't do on AT&T) or reflassh back to stock, you lose the fake system status. That means if you root your phone and try and get it replaced under warranty, if they reflash stock (which they always do) the custom system status will show and your warranty is out the window. So for now, if you root, expect that you DO NOT HAVE A WARRANTY!