Other than that, the only other thing that could possibly affect the CR would be the actual rater. The entire process is just a bunch of opinions of the rater. Some might feel trees could be a problem while another rater could feel that the trees are far enough away from the fairway, green, etc. that they shouldn't affect a shot. If there is a new course rater for the Florida State Golf Association this could be the reason.
A lot of those are measurements, too. The "density" is a subjective thing (because tree trunks could be identical, but if you're in South Carolina, you might not have a branch on a pine for the bottom 30 feet, while in PA, it could be like a Christmas Tree type pine tree with branches all the way to the ground.
But the distance from the center of the fairway, the fairway width, the rise/drop having to meet certain thresholds (and cover 3/4 of the green, IIRC - my manual is downstairs) and all that stuff is pretty objective.
The subjective things are whether a green is "relatively flat" or "severely contoured" (or in the middle), and even those have guidelines.
Not sure how true this is, but there is a course I play, that the rating was lowered. When I asked why, the course manager said it was done to keep up with newer club technology. In his opinion today's clubs make playing easier, hence the lower rating. Perhaps this is what happened at your course.
That sounds like they made their own rating and it may be unofficial.
Answered already, but basically they almost assume somehow that the golfer cleared the hazard and is playing the next shot from just across… with an adjustment of course because it's obviously not occurring per the guidelines. It's a work-around to stop a course rating from ballooning.