Our Scheduling team tried mightily to use CAPPM and MS Project in concert, and eventually gave up after encountering 2 major challenges:
1) There were defects in the integration that caused errors on certain projects, but not others. I personally created at least 5 CA Support tickets on behalf of the Schedulers, and the answer was usually "That'll have to be addressed in a later release." Also, to your point, the Schedulers encountered data changes and other inconsistencies that made them crazy.
2) The data content requirements to enable MS Project to fully integrate with CAPPM are pretty stringent. Resources, Charge Codes, Open for Time Entry values, etc. ... technically, they're not hard to do, but we had a lot of non-Schedulers building MS Project schedules that didn't conform to these requirements, so the Schedulers had to spend a LOT of cleanup time on the MS Project files before they could be uploaded to CAPPM. One of our Schedulers once told me that, when given an MS Project schedule, about 30% of the content could be uploaded as is, and the other 70% was just easier to do within the CAPPM GUI. All of that is absolutely not CA's fault, but it did make it difficult to use the full capabilities of the integration for non-technical reasons.
My 1-word recommendation on using MS Project with CAPPM is "Don't".