It does matter where the updates come from because HTC will slack off and stop supporting these low volume devices as soon as they can get away with it because it costs them money to test updates. If Google is behind it they have more responsibility to stock Android and I'm sure plenty of Googlers are enjoying these devices and want to maintain them.
To a certain extent I understand your concern and we won't truly know until it happens, but given that there's incredibly minute differences in the kernel of the HTC One compared to the Nexus devices it really can't possibly take that much time to test and update the software for the Google Edition smartphones. When 4.3 came out it was available for the HTC One some 10 days after Nexus smartphones received it. So, the testing and update process is obviously quick and simple. The only real difference between the One GPe and Nexus is that the One has touch sensitive buttons and HTC threw in BoomSound. That's very minor adjustments. All they'd have to test for is making sure those 2 things work fine.
Personally, I think GPe smartphones are safe for at least a year or two. Or, who knows, perhaps it's a contractual agreement with Google that GPe smartphones have to be maintained for a specific period of time. I don't imagine Google allowing any smartphone in the Play store that an OEM could chose to simply stop supporting it in too short of a time frame. Would make Google look just as bad since it's in their store and running their stock software.