at the end of the day if you think it sounds good then go for it mate.
if you were wanting a proper SQ(sound quality) system it would be a bit of a no no as the placement of the different frequencies will interfere slightly with each other and cause "muddying" of the sound. proper set up should be components up front ( mid driver angled slightly upwards an towards you, tweeter mounted around head/chest height ,again angled towards your head) and a sub/6x9's (running low freq only) at the rear.
one of the reasons you will have been told not to run the components in the rear shelf is that the sub will be using ALL of the air in your boot, so the components will be sharing airspace.that will result in the sub taking over the component and messing up the movement of the cone, resulting in the comp driver playing the wrong freq's and sounding distorted. this can be gotten around if you are intent on fitting them there, just box them in (leave a few inches from edge of speakers and about 4"deep from where the magnet will be) and they wont be affected by the sub.
hope that helps!