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To improve efficiency, you could consider partitionning your problem: Decompose your area of interest into several zones, run the process on these zones and re-unite the result. For your case, you could consider decomposing the input square into 4, for each of them, select the land polygons intesecting them (with a spatial index why not), running the union/...


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An option to use difference function with point geometries is using QGIS expressions with Geometry generator or Geometry by expression (see here for details) with this expression: difference ( $geometry, aggregate('points_2', 'collect', $geometry )) Expression used on layer points_1 (10 red dots) with difference from points_2 (6 blue triangles) ...


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No real solution has been found yet, but I got a workaround that worked quite nicely. I got rid of slivers around polygons in QGIS after a Difference tool by first buffering the feature by 5cm. For my case a slight inaccuracy in area was less important than getting rid of the "Difference slivers". The Difference tool also created some unwanted ...


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Add a check for polygons with an area below... let's say 30 sqm to your workflow (select by expression using area($geometry) < 30). Maybe 10 sqm, depends on your dataset. Select those, delete those.


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