GI Home is for RAC only and Oracle Restart is the standalone version, which you want to use.
It does not matter that you have already patched the DBs. Grid and DB are separate homes, even if on the same os user. They get patched separately. When you set your environment properly for ORACLE_BASE, ORACLE_HOME,PATH,..., (or better have separate os users) you can check with "opatch lsinventory" that you have selected the right home and what patches are installed in it.
You should use case 4, which will patch the restart home and check and then ignore the db home, as it already has the patches.
Alternatively patch only the restart home manually:
Readme - Patch Installation and Deinstallation For 126.96.36.199.x GI PSU [ID 1494646.1]
That note contains a section for manual patch apply, which can be done selectively.
My confusion is in the Table 2 of the doc Patch Installation and Deinstallation For 188.8.131.52.x GI PSU [ID 1494646.1]. In that table, it has the configuration GI Home in conjunction with RAC, RACOne, or Single Instance home. What does GI Home in conjunction with Single Instance home mean? Originally, I interpreted that configuration same as the configuration Oracle Restart Home. However, I believe it actually means using Oracle Clusterware for Single Instance Oracle Database.
"However, I believe it actually means using Oracle Clusterware for Single Instance Oracle Database."
Yes that's the meaning of it. You can create "normal" database instances on top of a rac.
In your case i would recommend to use opatch auto and select the grid home specifically like this:
/oracle/11.2.0/grid/OPatch/opatch auto /install/psu5 -oh /oracle/11.2.0/grid -ocmrf /oracle/11.2.0/grid/OPatch/ocm/bin/ocm.rsp
That will patch only the grid home and let the db home alone. Or follow section 5 of the note for manual patch apply for the grid home, that works also fine.