Generally speaking, if there are machines holes on an machined surface w/o threads in them in odd out of the way locations on engines and transmissions, they are normally used with locating pins during the various stages of machining the engine block and transmission cases.
The last picture once you install the transmission to engine block bracket, holes 5 & 6 must have bolts in them to properly seal the end cap. If they don't go through the transmission to engine bracket, they need to be installed before installing the bracket. Most if not all of the holes 1-4 will have bolts in them to the bracket.
Here is what the LS4 transmission to engine bracket looks like. Other engines use similar but different brackets.

[This message has been edited by fieroguru (edited 03-26-2023).]