^ STO originally was granted access to everything pertaining the prime universe, except the Narada, Kelvin and Jellyfish ships. These are still off-limits, but the others are now part of 25th century Starfleet lineup, and you travel into the Kelvin timeline for one mission.
So here we've seen a change in access in one tie-in.
Actually STO is allowed to use everything from XI and Into Darkness, CBS asked them not to use anything from Beyond according to one of the employees from Cryptic.
They just chose not to use those ships you mentioned. The Naradra is nearly 5-6 miles long, so it would have been too big. And small shuttle craft like the Jellyfish are not very popular.
The Kelvin is also an old ship, but they brought back the NX-Class and Refit as a 'replica', so they could use the same excuse for the Kelvin.
As far as anything I've read about it, Countdown is considered canon
AFAIK, that "fact" comes from an often out of context quote from one of the writers. He later said in the same interview that 'canon is up to the fans not him' or something along those lines.
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