Unrooting is a side effect of a major OTA. Because moto can't (easily) account for every combination of OTA a phone may have prior to a major update, the easiest way is to wipe the system partition clean and put the update in a fresh install. It's like trying to update from XP to W7. Too many vairiables to update so a fresh install occurs. The Easter Bunny said so.
-------------------------------------------------------------------------
I respectfully disagree. Motorola, more than any other phone manufacturer seems to be personally INSULTED that the people who buy their product have the temerity to *think* that they know better than Motorola when it comes to what belongs on that phone. Motorola has shown an arrogant disregard for the rights of the end buyers ever since the release of the unlocked D1 and the fact that they consistently ferret out the keys that were used to unlock (root) the phone receiving the OTA update, and close that door.
Fortunately, the development community has managed to stay one step ahead of Motorola and the other manufacturers and manages to undo the damage inflicted by the non-accidental, VERY intentional un-rooting caused by their tainted OTA update. As I've said elsewhere, in different threads - why waste your time with an OTA update, when you've got many custom roms that offer all of the good, cool features months in advance of the OTA release? By the time it arrives, it's old news.
--------------------------------------------------------------------------
Not absolutely. You can still get OTAs when rooted. In some cases you lose root. In others you don't but the OTA will succeed. As you say, if you also install a custom recovery, custom ROM or remove certain bloat the OTA will likely fail. Not all phones even prompt to accept the OTA. Some automatically install it. Samsung S (non Kies) for example. Santa said so.