Sorry @KC_Baltz for the veeeeeery long time before answering you. This thread went completely out of our radar.
I just created the following ticket to handle it: SONARJAVA-3499
Note that the fix is currently planned for version 6.7 of our Java analyzer, which will be available only on SonarCloud and SonarQube 8.5 (expected to be released at the end of September). For LTS users, it won’t be possible to benefit from it.
However, as tested on my local SQ instance, a possible workaround is to configure the rule by settings its customInjectionAnnotations parameter with javax.persistence.PersistenceContext, which will make the issue disappear.