I don't think the engineers make their decisions on whether it's a good idea or not. It's usually that they have 2 settings and they pick one for the sake of it in a 50/50 toss up.
There is more at play here other than the setting being checked, as I can't see it being a major player in any slowness within InDesign. The only issue would be if they copy something from InDesign and it's copying a PDF as per the preference.
If the PDF is then a complex vector dense it could cause issues - maybe?
But - I have never had an issue in this area so I am just guessing.
However, the InDesign to Photoshop methods are clear enough - it's not really a good idea to copy and paste from InDesign to Photoshop or vice versa - so working that out of the workflow makes sense.