Reapply "Apply pending transactions always"

This reverts commit 71d8423836dfbfb01e093da63baec54f3e786375.

Track if pending transactions have already been applied and only
apply the workaround if the transaction is not empty.

Flag: EXEMPT bug fix
Test: repro in bug
Bug: 334901521
Change-Id: If2b7e54bc4fe2582fd72a6f8c2511671acce2cfa