Starting with 3.10.0b1, Shell is being reworked in ways that make this issue, as formulated, out of date.  Solving the indent problems means that prompt must be removed from the first line of interactive input.  #37892.  The initial solution is to put >>> and ... prompts in a sidebar.  #37903.  The rules out customization.  A planned alternate solution is to put the prompt on a line by itself above interactive input.  A followup issue could be customizing the isolated prompt by a setting in the options dialog.