Hey @PhilvK
I do not believe that the extrusion got joined because of aligning it...Align tool does not join element and extrusions do not join automatically (it's not coded in Revit, neither for Extrusions nor for any other 3D modeling tool such as blend/sweep...etc). I believe that the Join happened before/earlier and it just appeared when you used Align
What might have happened is that the Join Geometry was envoked by mistake and you applied (unintentionally) Join Geometry sometime before the Align. In this case...at the first instance you wont see the two extrusions joined...After you applied Align then the top segment of the bottom support got joined with the worktop.
To double check...when you flex the support down...check the properties palette/dialog under Identity data - it does not show it is a Solid Extrusion even when it is detached. Extrusions lose that property when they are joined using Join Geometry.
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