P: Merging layers or layer groups deletes pixels outside of image window.

Merge Layers (Cmd+E) with no group included in the selection will preserve off-canvas pixels.
Merge Layers (Cmd+E) with group(s) included in the selection will remove off-canvas pixels.
Merge Groups (Cmd+E) removes off-canvas pixels.

A workaround to preserve off-canvas pixels when merging group(s) or a combined selection of group(s) and layer(s):
Ungroup Layers (Shift+Cmd+G), Merge Layers (Cmd+E)

You may be mistaken.
Edit: Merging Layers that extend beyond the Canvas simply does not seem to behave as the OP claims.

Are Layer Masks involved?