well they will probably have you drill holes behind the door panel, where no one will see, so I do not think this sounds odd at all. Auto manufactures have been trying to make their audio systems more and more incompatible and less standard to make it hard to not pay $1,500 for a crappy oem system and then just go to a shop and get something better for $500. Just another example
Sounds fine to me though. No if these were visible holes, that would sound nuts. And drilling holes through speakers? Usually speakers have the cone (obviously woulnd't drill through that) and then a steel rim that goes around, I don't imagine drilling through the rim would be very easy. And that probably won't work anyways.