This is a good question.
The main reason is that all of my standalone projects are fitted with 4-pin plugs that with a wee shield+cable that I made can be programmed. Sure, it would be possible to make another and switch it out depending on which box I'm currently programming (or buy a standalone programmer for these boxes) but I've seen a number of tutorials out there that make this 'bootloading-and-programming-a-standalone-644-with-arduino-IDE' seem trivial, so it seems like I should be able to get it to work...
Thanks for your replies