Hi Scott,
the core plug is closing off the lower end of the engine main clutch actuation lever's vertical shaft and any blackish oil in the dry main clutch compartment can be due to running the main engine with a clogged crankcase breather and/or a failed transmission input shaft seal if it is clear transmission oil leaking out the main clutch compartment drain plug.
The other indented spot you show, depending on its alignment to the rear divider wall in the trans. case, could be another core plug used to hold a dowel in place to secure a bearing race into the transmission case for the lower transmission shaft rear bearing.
If it is not a core plug then it could be a casting flaw that is easily fixed by drilling and tapping the flaw with a suitable sized thread and inserting a suitable plug like 1/8" National Pipe Taper or 1/4" NPT as needed. This is a method we used at the Dealer for such issues. Even say a 3/8" Unc. or Unf. bolt with suitable sealant would suffice if you do not have a suitable NPT tap in your kit.
Cheers,
Eddie B.