This is the same as in the previous version, but there was also the other radial part which didn't have this problem. Basically, in order to get the same orientation as the command pod, you have to stick AR202 on the left side of the rocket, instead of on the front.

Controlling from a radial mechjeb part attached to the heavy lower launcher stage can be useful to reduce wobble, and putting an appropriately rotated one on a rover allows setting navball to an orientation more appropriate for driving.

Closing this as an old MechJeb issue. Many MechJeb issues have had little interest in years, have been fixed for years, do not include adequate replication steps, refer to old problems which are no longer applicable, or are difficult to determine what the problem is. This issue is being closed for one of those reasons. We apologize for any inconvenience, but keeping the TODO list tidy helps the developers.

If this bug/issue is still a problem, please open a new issue. For bugs please try to include a Minimal, Complete, Verifiable Example that explains all the steps required to replicate the issue. A link to the KSP.log file should be ideally included, but is often not sufficient information. Screenshots or short videos are often the best way to show a bug.