I just tried to AOIs that use a common side and one common corner and it reports the two volumes in the two AOIs with no problem. It does not flag that the two areas overlap in the report
If I then move one side of an AOI boundary so that it does overlap the other one then it flags that the two AOIs overlap and that the volumes may be erroneous etc. as a result.
The fact that we report the issue of potentially overlapping AOIs is there to protect you as a user from double counting quantities, as we have seen many projects over the years where AOIs did overlap and people were reporting erroneous volumes.
An overlap can easily occur if the polygons are multinoded. I agree that if you draw two rectangles and use two corners and you accurately snap the corners using End Point snaps then that should not happen, and in my quick test data set it appears to be working correctly, however data varies from project to project so there maybe something unique about your project which is flagging the issue you are seeing - if you want me to take a look, please share your project and I will see if I can see what the issue is.
For example if you drew as a linestring and you just happened to double click at the start of the line you may have two nodes really close together - maybe something like that happened? If you used the Lines to AOI command to create the AOIs - maybe somehow that added in a small rounding error to create a slight offset that makes the lines overlap slightly.
If you are sure that there is no issue with the AOIs then the warning is just that - a warning and you can ignore it in the report if you are sure the data is good and clean.
It would be good to know what the issue is with the data - can you send me just the AOI lines as a VCL file (email@example.com) so that I can check it out for you.