I've had the same problem with this patch for SQL Server 2008 R2 SP3 (Version: 10.53.6000.34), but maybe I found the root cause for this.
There are multiple checks for the baseline package and version during the setup routine. While all others succeed to find the right values, the check on the line prior the line you posted was the culprit.
My log file had the following:
2016-09-19 16:57:26 Slp: Patch Id: KB3045316_sql_engine_core_inst_Cpu64 - The baseline msi is not installed. The patch package is ignored.
2016-09-19 16:57:26 Slp: Patch Id: KB3045316_sql_engine_core_inst_Cpu64 - Detail description of this patch package is: PatchId=KB3045316_sql_engine_core_inst_Cpu64 PatchVersion=10.53.6220.0 BaselinePackageId=sql_engine_core_inst_Cpu64 BaselineVersion=10.53.6000.34; PatchFileName=sql_engine_core_inst.msp PatchCode={C83DA2A5-0249-4330-A786-B5E1650FB6AB}
It looks like the check is performed with help of Windows Installer service and full restrictions for a minor upgrade patch, which means the product code of the un-transformed baseline package must match the target code of the patch. In my special case it was {93A57276-C398-4E0C-9D08-B02815E19AD4} for the product code and {13E296DD-0186-4DE3-8133-145C1A3EC691} for the target code:
Because the Windows Installer service was used for the check you get the errors on the application event log if something goes wrong.
So far so bad. Now it comes to the strange part.
The setup routine just ignores the last check and continues to install this patch file by manual instructing the Windows Installer service how to apply it (lower restrictions for the QFE patch).
Here is the log for this part:
MSI (s) (14:74) [17:03:22:857]: SequencePatches starts. Product code: {FBD367D1-642F-47CF-B79B-9BE48FB34007}, Product version: 10.50.1600.1, Upgrade code: {1CBCA79C-7BD0-4F4F-B927-EED77B249CE1}, Product language 1033
MSI (s) (14:74) [17:03:22:857]: PATCH SEQUENCER: verifying the applicability of minor upgrade patch {783E8847-EE12-4DB3-969A-15490E01B24E} against product code: {FBD367D1-642F-47CF-B79B-9BE48FB34007}, product version: 10.50.1600.1, product language 1033 and upgrade code: {1CBCA79C-7BD0-4F4F-B927-EED77B249CE1}
MSI (s) (14:74) [17:03:22:857]: PATCH SEQUENCER: minor upgrade patch {783E8847-EE12-4DB3-969A-15490E01B24E} is applicable.
MSI (s) (14:74) [17:03:22:857]: PATCH SEQUENCER: verifying the applicability of QFE patch d:\358e4ddee3e7f3f7544485bf548c\x64\setup\sql_engine_core_inst_msi\sql_engine_core_inst.msp against product code: {93A57276-C398-4E0C-9D08-B02815E19AD4}, product version: 10.53.6000.34, product language 1033 and upgrade code: {1CBCA79C-7BD0-4F4F-B927-EED77B249CE1}
MSI (s) (14:74) [17:03:22:857]: PATCH SEQUENCER: QFE patch d:\358e4ddee3e7f3f7544485bf548c\x64\setup\sql_engine_core_inst_msi\sql_engine_core_inst.msp is applicable.
MSI (s) (14:74) [17:03:22:857]: SequencePatches returns success.
MSI (s) (14:74) [17:03:22:857]: Final Patch Application Order:
MSI (s) (14:74) [17:03:22:857]: {783E8847-EE12-4DB3-969A-15490E01B24E} -
MSI (s) (14:74) [17:03:22:857]: {C83DA2A5-0249-4330-A786-B5E1650FB6AB} - d:\358e4ddee3e7f3f7544485bf548c\x64\setup\sql_engine_core_inst_msi\sql_engine_core_inst.msp
...
MSI (s) (14:74) [17:03:31:217]: Product: SQL Server 2008 R2 SP2 Database Engine Services -- Configuration completed successfully.
In other words:
The setup routine produces ugly errors in the logs, but the installation succeeds without errors.