Not sure what you mean; the overlap of infill and outlines works to keep my prints "airtight" and doesn't cause any issues in the physical prints.
I don't see how those settings would cause the support structure have holes in it due to the manually place supports overlapping. Or how that was not a problem in the previous version but is in the newer ones.
The supports intersect with the model because the support designs are squares, and I try to place it so the supports are where I feel they're needed the most/best.
There's a setting to keep the supports X far from the models surface, so I would assume this is expected.?
Supports end up overlapping because I want supports on some bottom surface but not on others (like I don't need supports INSIDE pin holes, but I do need them on that part of models base beneath/around it) or I want to add supports to areas that the auto-support didn't generate.
The factory files I linked to are exact same file opened in different versions of the program (Which they both seem to share the same account/source file, so it automatically opens the same file with the same supports. )
https://drive.google.com/file/d/16X23gA ... sp=sharing
Check the linked file out, made in v 4.1.2, and go to layer 28: in it, you can see that the manually placed ones have gaps where they overlap. It seems if over an X amount of the supports overlap it generates a hole. (On this layer you can also see where the automatically placed ones first surface layers are being generated as separate parts. In the next layer they are combined. )
I honestly believe something was changed on how the support structures are being generated after v4.0.0, since it only started having this issue after that version, and because it still works correctly in this version using the same file that doesn't work in the newer ones.