On Land

Environment Information
At Rill Architects we run ArchiCAD on macOS. If you work at Rill, this is your stuff. If you don't, but you work in ArchiCAD, you may find something interesting. Anybody else, I don't know.
Profile Patch 1
This is a complicated condition. It's surrounded by ordinary modeling elements, but it's difficult to weave those elements together such that it all cleans up and looks correct in section.

Here's the ordinary elements by themselves. I put in some detail objects for clarity:

Profile Patch 3
The joist deck slab is basically right. The concrete slab needs to reach in to bear in the foundation wall. That edit is easy, but then we need concrete below the slab to reach the top of wall, and above to reach the sill plate behind the veneer.

The top of the concrete wall is in the right place for the joists, but it's part of a composite with the stone veneer that needs to reach the bottom of the slab. Likewise, the frame part of the upper composite is right, but the stone needs to come down.

There are several ways to solve this with walls and slabs. I'm not going to go into them, except to say they are all rather unpleasant, typically involving 3-5 elements, some of which will be new composites. Sad work, especially when you have to take the whole mess around a corner.

An alternative would be to use fewer elements, get it looking OK-but-not-great, and then use a patch to make it pretty. As you know, you create a patch from existing geometry, and then use 2D editing to force it to look right.

(To be clear, I'm not against patches. They are hacks, but often essential hacks.)

Here's the thing though: If you're going to push fills around to make the condition look right, why not do it in a custom profile? It's still a 2D shortcut, but you end up with a 3D piece you can use wherever you find the condition. It will miter around corners and generally behave like a proper modeling element, displaying correctly no matter where you view it.

A custom profile can be arbitrarily complex, made up of any fills in any shape, and when it's placed it will clean up in section to the like fills it touches. Its surfaces will clean up to like surfaces in elevation.

Profile Patch 4
In this example there are six fills, all cleaning up properly with the adjacent elements. I changed the background color for clarity, but you can still see the cleanup is working.

Profile Patch 5
1 is the concrete which completes the slab and forms the stem wall. 2 is the stone which matches the composite skins above and below. 3 is Empty Fill meeting the empty composite skins. 4 is a special optional Empty Fill. It meets the joist deck slab. Of course, you could extend the slab 1/2" to fill this space. But by putting this filler in the profile, I can keep the slab at the inside face of the frame wall, which is an easier edit.

Such a profile could used with a wall or a beam element. Use a 3D-only layer such as A Wall3. It's probably easier to place the wall/beam on the lower story in this case. If you use a wall for the profile, set its Floor Plan Display to 'Overhead All' so it stays transparent.

Conclusion: If you're facing a multi-fill section patch, see if you could use similar fills in a custom profile instead.