It's not strange to me at all, since the Rift was an RTD concept and it's Moffat's show now. Moffat has taken the show in his own direction and has rarely brought back any story elements from the RTD era.
Doctor Who has never been a franchise known for strong continuity or internal consistency. The specifics get reinvented all the time, so it's wisest not to dwell on them. It's best if you look at it in a more impressionistic light, or as an epic myth. The details of a myth change depending on the teller and the era, but the essentials remain.
But if you want an in-universe explanation, keep in mind that a couple of more centuries have passed for the Doctor than for us. And didn't the Cardiff Rift turn out to be one of the cracks in time or something? Wasn't it closed several seasons ago? So the Doctor would've needed to find a different power source, and would've had plenty of time to figure out how to access the Eye.
Well, yes, but rift energy is still a relatively memorable thing (Boom Town
and the Moffat-era The Doctor's Wife
). I think they could have expended a line or two to clarify.
Regarding the crack, I think RTD did say in interview that he was thankful to Moffat as it meant he didn't have to close the Cardiff rift - it could just be another crack, even though he hadn't planned it that way. That raises the question, of course, of whether The Cardiff rift has now been erased from the timeline of the Whoniverse.
Well, that's a given. Stars don't collapse into black holes unless they're at least 30 solar masses.
...or get a push from a stellar modifier like the Hand Of Omega, which was seemingly how the original Eye Of Harmony was created.