It's pretty clear that you've been tweaking Open Rocket to get good matches (!%-2% error), then you do just a few runs on RASAero II and say there is a 10% difference. Tweaking RASAero II will also get you to 1%-2% error.
Are you adjusting the surface roughness or launch angle in Open Rocket? Are you adjusting the launch angle to match a measured downrange distance? A tweak running Open Rocket to better match altitude data may be covering up a less accurate model. Perform the same process with RASAero II, you'll get down to 1%-2% error. From your posts above you've already eliminated most of the 10% difference by surface roughness and all turbulent flow settings, you have to dig deep to make sure you are really running a one-to-one comparison between RASAero II and Open Rocket.
I'm not making a criticism here. Adjusting your simulation model is a key part of the altitude prediction process. Jim Javis's Mach 3 rockets have been coming back from flight with less thermal damage than other rockets. For his rockets the surface roughness setting in RASAero II is different than for other rockets, Jim has calibrated it from prior flights. It makes his predictions for future flights more accurate.
I'd recommend tweaking RASAero II until you have the same 1%-2% match, because the lack of variation of thrust with altitude in Open Rocket is going to cause you problems as you move from near sea level to 4,000 ft at Spaceport America.
There are two possible strategies. The strategy above is to have the most pessimistic altitude prediction, in which case I would use the rough camouflage paint surface roughness setting and all turbulent flow. This way you make sure you never undershoot.
The strategy I proposed is that you should plan to overshoot in altitude, and the real issue is whether your modulating drag producing device has enough authority (like control authority) to generate enough drag to overcome the most
optimistic altitude prediction.
Remember, overshooting by too much, and your drag modulating device can't overcome the overshoot, is also a potential failure mode.
So those are your two possible strategies.
As you are doing, I strongly recommend you perform flight tests to verify your CD change as a function of how you are modulating the drag.
As a note, a fellow aerospace engineer co-worker of mine who went on to become a University professor, had a team in a contest like this where they were the first to use a real-time drag modulating device to hit a specific altitude. They won the contest. I won't provide details here, this is of course a competition.
What really impressed me was that they put the rocket with the drag modulating device in a wind tunnel (!!!) with the drag modulating device at different settings for different wind tunnel runs. You'll do fine with flight tests, but I was really impressed that they put the rocket in a wind tunnel.
Charles E. (Chuck) Rogers
Rogers Aeroscience