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Related issue #22893 is about __future__ statements in startup code having effect on future interactive input in the same way as it does with Python itself. I think a pure Shell start/restart (cntl-F6) should be handled separately from a restart that is a side-effect of running an editor file. There is a separate proposal to specify an individual file's startup condition (sys.args + STARTUP file). For Shell restart, a possible reason might be to get rid of the effect of a STARTUP file. Since ^F6 is rarely used (I think), asking whether to include the STARTUP might not be too intrusive.
I think default behaviors should follow Python, though we can add more. On the other hand, Python has startup options not currently available with Idle.