It turns out that the bug is indeed not in Org, but in Emacs.  The part of 
combine-change-call which creates the undo-list element was totally 
broken.  For example, with a buffer-undo-list like

<undo element 1> <timestamp> <undo element 2> <timestamp> nil <undo element 3>

ofter body has been evaluated, the buffer-undo-list after 
combine-change-call is

(apply ... #'undo--wrap-and-run-primitive-undo ... (<undo element 1>)) <timestamp>  <undo element 2> <timestamp> nil <undo element 3>

which is clearly wrong, because <undo element 1> and <undo element 2> 
should be considered as a single undo step.  IOW, after 
combine-change-call buffer-undo-list should be:

(apply ... #'undo--wrap-and-run-primitive-undo ... (<undo element 1> <undo element 2>)) nil <undo element 3>

Patch attached.