Got my answer (I hope) :) It looks like the nominee change only required 53 votes to change a rule, whereas the change to the CR would require 60. so it isn't using the same vote count and appears to be a deceptive statement.

I think where you're getting a bit mixed up is in thinking of what the Senate is currently contemplating as a "change to the CR."

There's two different votes that one needs to think about:

1) The vote on the underlying item (ie. the vote to confirm a nominee, the vote to pass the CR); and
2) A vote to change the Senate rules governing the vote described in #1.

Prior to the "nuclear option," many of Trump's nominees were being held up by filibuster. Because those votes (like nearly all votes) were subject to the 60-vote cloture requirement, they could be filibustered. So most of those votes were failing 45-53 (or whatever).

The Senate GOP decided to change that rule. They voted on an amendment to the Senate rules to exempt nominee confirmations from the cloture requirement. Amendments to the Senate rules require only a straight up majority. They passed that amendment by a 53-45 vote, and created a new rule for confirmation votes. The substantive confirmation votes themselves then proceeded to get voted on and passed by simple majority.

Votes on a CR are still governed by the general rule requiring 60 votes to end a filibuster. So the Senate has been unable to pass the CR itself. The Senate has the ability, as always, to consider a vote to change the Senate rules again - this time, to eliminate the filibuster for CRs (or budget matters more generally). They could pass that rule change by a simple majority vote. But they can't pass the CR (technically they can't invoke cloture on the debate on the CR) by a simple majority vote, unless and until they amend the senate rules first.

Since amending the Senate rules to remove the filibuster for a given matter has vastly more far-reaching consequences than simply voting on the matter itself, there are fewer votes in favor of nuking the filibuster for budget items than there are for simply passing the CR. Although Thune certainly has 50+ votes to pass the CR, he does not have 50+ Senators who would be willing to amend the rules to eliminate the filibuster for CR's.