But the question is, what's more official? A chart made with what seems to be just preliminary information that would change later, and was not meant to be seen up close, or an official publication like the Encyclopedia
Well, let's have a quick look at the Enc. ship list:
Some things were obviously made up to fill the gaps. Like the registries and classes for the Antares, Carolina, and Archon and pretty much all the Constitution-class registries. Some registries and classes are just plain wrong, like 1937 for the Saratoga, 59983 for the Raman and Olympic-class for the Biko.
Considering all this, I'd say this chart is more official than any unverified information from the Encyclopedia. It doesn't contain any silly names and at the time TMoaM was aired, the only problematic ship on this list is the Yamato.
with information that he clearly wanted to have supercede this chart?
That's not so clear. Maybe this chart got somehow lost and he invented new registries to fill the gaps.
BTW: The Yorktown also appeared on the DS9 Whispers shiplist.