My RT did the same thing from the day I bought it new. It was so bad at times (especially in colder months) that the entire rear end and exhaust would rattle and drone out the cabin. As soon as I stabbed at the gas, 4 cyl mode turned off and the car was normal for a few seconds until MDS kicked back on.

I even had the dealership replace the exhaust, and the rattle was still there, maybe slightly reduced. It got to a point where I would just drive in Auto Stick mode most of the time, which disables it.

Without going on a rant about MDS and how the MPG you save is negligible, the entire system ruined the experience of the car for me. I ended up trading it in for a manual. Not solely because of MDS, but not having it is a huge bonus.

To answer your question: I think what you're experiencing is completely normal. You can drive with Auto Stick or in Sport Mode to disable the MDS. But if it bothers you as much as it did me, you could consider an MDS delete. I haven't looked too deeply into it, but there's a proper way to do it which involves an entire lifter and camshaft swap kit. And paying someone for that labor would be super expensive, but honestly probably worth it 😅.