
Here's a clear step-by-step guide for creating a morph effect from
cube to pyramid using Blender Geometry Nodes. You'll need to store
transformation data beforehand so you can apply it individually to
each cube instance:
1 - Save the Delta (Transformation Data)

Capture and store the variation that each vertex of your cube needs to undergo to transform into a pyramid as an attribute.
Add a Vector Math node set to Subtract,
Subtract the output of your "pyramid transformation math" from the original cube position
Store this difference using Store Named Attribute called "Delta"
[Set it to Points domain and Vector mode]
This delta represents the "movement vector" each vertex needs to
follow during the transformation.
Set Position Node no more neceserrally here!!
2 - For Control the Transformation

You'll need to store another attribute with the distance from your Empty object to each instance to control the transformation.
Create a setup using Geometry Proximity based on your Empty object
Store this in Store Named Attribute as "Dist"
[Set it to Float type and Instances domain]
Important: Create this now, before converting instances to individual
meshes. This approach gives you the effect you're looking for, though
you could do it later for a slightly different deformation pattern.
3 - Convert Instances

This crucial step individualizes each instance so the transformation can happen independently.Use a Realize Instances node to convert all instances into separate mesh objects
4 - Morph Objects

Apply the actual transformation to your geometry. Use a Set Position node connect your previously created "Delta" attribute to the Offset input
This will move each vertex according to the stored transformation data
Control the radius of influence of your Empty object using various mapping nodes. Use nodes like Float Curve, ColorRamp, or Map Range (Map Range works well for simple cases)
Connect your "Dist" attribute to the Value input
Adjust the From Min and From Max values to define the influence area, and scale your Delta for Map Range output.
The result is a wave-like morph effect that propagates outward from your Empty object, smoothly transforming cubes into pyramids based on proximity.