Mad (Flt) Scientist,
To answer your second question first, the Operations Manuals that I've produced and alluded to PROHIBIT the use of intersection departures when General Charts / Tables are used.
To respond to your first question, "do all the crews realise exactly what you're doing", probably not. Whilst well written Operations Manuals are produced, and recurrent performance refresher courses etc. are carried out, there's still a significant number of pilots 'out there' who, having passed Performance 'A', promptly put it into the 'tick in the box' category and hope that they never need to use it. Methinks that the number of very basic performance related queries / responses on Pprune's pages are indicitave of this.
The best that we can do is produce the best possible performance material, training syllabi, and guidance to trainees, and hope that their professionalism is such that they would studiously apply it.