Rice,
I am a gal who likes to have kiddos follow the guide's plan as much as possible, as it makes it clearer for me and for the student to know what to do!
With that in mind, since your son did CTC's science this year and was able to complete it successfully, I would be inclined to do RTR's Earth Science next year for a couple of reasons. First, I think that earth science is not covered as often in high school and is actually a science that relates to day-to-day life more readily than many other sciences. Secondly, I think the progression of skills from CTC to RTR's science is more incremental, rather than jumping way ahead to a science in a future guide at this juncture while he is still honing so many needed skills.
Bearing in mind that he has already done the Astronomy book, I would first consider whether he read this book to himself or whether you read it to him. It is quite different to read one's own material. Another thing to consider is how long ago he did this text. That will also make a difference as to how redundant simply following the HOD plan for science would be. Next, I'll share that we do provide alternate experiments to do along the way instead of those that are super involved supply-wise in the Apologia text, so there is a different flavor to the way we use that text.
If you did feel that using the Apologia text is redundant, and bearing in mind that this is your son's last science year prior to high school, you could consider following all of the Earth Science plans in the RTR guide with the exception of the Astronomy book (which would mean starting partway through the plans in RTR). Then, at the end of the year, you could do the Evolution: The Grand Experiment study to finish out the year of earth science (following the plans within the MTMM for that). This plan is more convoluted than I would like, but it would give you more of what you are seeking with less overlap and would provide you with a truer earth science year.

It would also allow you to complete one science each year, making it easier to stay on track and less confusing.
So, then the plan would look like this:
8th Grade: Earth science (using RTR's plans either as written or use without Astronomy and add Evolution: Grand Experiment from MTMM at the end of the year)
9th Grade: Do either Rev2Rev's Advanced EE and Inventor Study or IPC from the World Geography Guide (This will provide the typically required physical science/IPC type credit.)
10th Grade: Do Biology from the World History Guide (and also do Total Health from the World History Guide)
11th Grade: Do Chemistry from the first American History Guide (at this point beefing up MTMM's chemistry could also be an option if the Chemistry from the American guide seems too difficult)
12th Grade: Do HOD's final science option from the last American History Guide (or omit science this year, if not headed to a science-related field as all needed credits will already have been earned in science... typically one physical science/IPC, one biology, one chemistry, with a minimum of two - three labs sciences)
I know this plan means he will always work out of a different guide for science, but this plan also incrementally raises the skill level science-wise and has a more seamless progression that will be of help to your son.
Blessings,
Carrie