This is the expected behavior.
When a log is saved, it checks to see if A) there are areas referenced, and B) the geometry is empty. If so, then it copies the geometry of the referenced areas into the geometry of the log.
But if B is not true (and there is geometry on the log already when the log is saved) then it will NOT copy the area geometry. It ONLY does that if the log geometry is empty.
If you draw a geometry and then save the log, then it assumes that you wanted that specific geometry, and does NOT copy the area geometry.
The only way to have both right now is to do like you said:
If I select the area first and save the log record, then if I draw the polygon, it takes both.
Notably, this is a little bit more “smart” in farmOS 2.x… but still would not work the way that you are describing. In 2.x, farmOS basically tries to determine if the geometry is a “custom” geometry or not. If it’s custom, then it doesn’t touch it. If the geometry is equal to that of the areas, then it will reset the log geometry if the area references change.
It sounds like you want to be able to have both a “custom” geometry AND the area geometry. There’s no easy way for farmOS to know that that is what you want, unfortunately.
This is the first time I’ve heard someone request this particular behavior (saving BOTH the area geometry AND a custom geometry). Can you describe why you want that? It’s hard to imagine a situation where you would so now I’m curious.