The x-height and overall blocks of letters are predefined in a standardized typeset. It is harder to distinguish between very similar looking letter blocks. E will always look like E in a typed document.
This is not true for a handwritten document. No matter how meticulous a writer is, there are subtle variations between letters and effectively the monotony is broken.
In the lowercase typed document, the ascenders and descenders have a standardization again. This helps our eyes to track the locations. Hence it is easy when a typed document is in lowercase.
On the other hand, the ascenders and descenders for handwritten text varies and does not really help the reader. In addition, the handwriting may jump between normal lowercase and running script at times, which makes lowercase handwriting even more difficult to follow.
Considering these two aspects together, handwritten All-Caps becomes more legible then typed one.