Its a simple list.... if you've done any of the following, OTAs will fail:
Install a custom recovery
Root
Modify your system image in some way (custom kernel, custom boot image, etc)
The OTA has a bunch of system checks that it goes through before it loads.... not because they don't want you rooting your phone, but because they don't want a stock OTA stomping all over your phone and busting it all to pieces. So those OTA checks are to protect YOU.
But since you've already set up an environment that can flash the full factory images, you really don't need to worry yourself over an OTA. You can flash newer factory images without blowing away your system data (which the flash_all command will do by default).... It might take a couple of extra steps, but you've already got passed the 'hard' part by setting up ADB and fastboot.
Plus, OTA updates tend to lag a bit after the full factory image.
By the way, I have a feeling that we've seen the last of all the loony carrier specific factory images. It got out of control with the Nexus 6 and LP with all the different flavors.... But I think Google is just rolling all those specific bits into the main branch.... WiFi Calling for T-Mobile, the various different VoLTE implementations, Project Fi, etc. I think Google got annoyed at what turned into mass confusion.