From my understanding it's no plot inconsistency. At least it's explained in the episode.
In one of the earlier episodes, the Doctor hides the TARDIS by shifting it out of time by a second or so, which causes it to disappear. To me, it's time locked in some way. Could this be the same or a similar effect?
However, I don't think the Time Lock and Gallifrey being hidden (or returning according to Rassilon's plans) are the same in this instance.
During The Day of the Doctor once all three Doctors arrive in the barn there's the following short conversation:
WAR DOCTOR: Go away now, all of you. This is for me.
DOCTOR 10: These events should be time-locked. We shouldn't even be here.
DOCTOR 11: So something let us through.
To me, this clearly refers to the Time Lock existing already, so there's no way the Time Lock being the effect all incarnations of the Doctor create at the end of the episode.
For some reason the Moment was powerful enough to "open" the Time Lock for the TARDIS's to materialize (and for a fez, War Doctor, and War Doctor with a fez to travel there and back again as well).
The episode also seems to refer to the events from The End of Time. In the first scene featuring some kind of war room on Gallifrey:
ANDROGAR: The High Council is in emergency session. They have plans of their own.
GENERAL: To hell with the High Council. Their plans have already failed. Gallifrey's still in the line of fire.
To me the High Council's plans would be exactly the events we've seen during The End of Time. They've failed (they obviously planned bringing back Gallifrey without the Daleks that were in orbit). While this could be some kind of general plan or strategy, I think this is indeed the attempt at bringing Gallifrey back. So this happened and it's not somehow lost in an alternate timeline that never happened.
But even if you consider Rassilon referring to the effect the Doctor(s) created, it would still make sense. It's possible, the High Council didn't listen to the Doctor(s)' messages or didn't believe it would work. So they might not have known that the Daleks have been destroyed. I think there's even one scene showing the outskirts of a city with destroyed Dalek ships, although I'd have to watch the episode again first.
As a minor note: The only plot inconsistency that I'm aware of and that is valid I think, would be the whole "still the same sonic screwdriver" part. There were two or three instances during the new series where the Doctor had to replace his sonic screwdriver. I don't think he'd have been able to somehow transfer the software (e.g. once half the screwdriver being eaten by one of the flying sharks and the other half being kept by the young boy in his bed stand).