#05AB1E, 10 9 bytes

¶¡RζðмζR» 

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or with alternative start:

.BRøðмζR» 

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Similar approach as @Dennis♦' Pyth answer.
-1 byte thanks to @Emigna replacing ðõ: with ðм.

Explanation:

¶¡ # Split on new-lines R # Reverse the list ζ # Zip/Transpose with unequal-length items (with space filler by default) ðм # Remove all spaces ζ # Zip/Transpose unequal-length items (with space filler) again R # Reverse the list again » # Join the list by newlines, and output implicitly 

Alternative explanation:

.B # Box (implicitly splits on new-lines and appends spaces) ø # Zip/Transpose with equal-length items # Rest is the same 

05AB1E, 10 9 bytes

¶¡RζðмζR» 

Try it online.

or with alternative start:

.BRøðмζR» 

Try it online.

Similar approach as @Dennis♦' Pyth answer.
-1 byte thanks to @Emigna replacing ðõ: with ðм.

Explanation:

¶¡ # Split on new-lines R # Reverse the list ζ # Zip/Transpose with unequal-length items (with space filler by default) ðм # Remove all spaces ζ # Zip/Transpose unequal-length items (with space filler) again R # Reverse the list again » # Join the list by newlines, and output implicitly 

Alternative explanation:

.B # Box (implicitly splits on new-lines and appends spaces) ø # Zip/Transpose with equal-length items # Rest is the same