Your correct in your thinking. Actual load as it will be used is the weight that matters. One thing to remember is that while the weights may be similar on the two units, the actual amount you put in them may vary more than you first think. The one with the higher CCC likely has bigger tanks which could make a difference in your final load out.
So long as you are mindful of what you actually have in the rig compared to your vehicles limits you should not have an issue.
And in some cases it may be of great benefit, such as in a bunkhouse unit with a growing family. You could buy and use the trailer now, and increase your truck size to accommodate the families growth in a year or two. As I said above, just be mindful of what you actually have in the rig.
