It's normal , I also have the same behavior , it's not a conflict. and the most accurate as you said,that mentioned at
SharePoint Designer. but in fact, no one accurate than other each one represents specific information as I mentioned below.
the version number at control panel is represented the default build number of product installation , and to ensure that check my installation version number that is identical to your version. because it's the same product.
the version number at SharePoint Designer is the build number of SharePoint Designer
latest update. if you applied update as Service Pack it will be reflected at SharePoint designer not at control panel
- SharePoint Designer Version