@1:1: Arduino is just a bundle of an AVR prototyping board with a somewhat standardized pin layout, a processor with a preflashed bootloader and an IDE.
You can do all of the following:
1) Use the Arduino IDE to develop for other boards (as long as the processor is supported).
2) Use the Arduino IDE to flash targets WITHOUT bootloader using an ISP. Especially you can throw out the bootloader once you have an ISP
3) Use the Arduino IDE to flash "naked" AVRs (if you have an ISP).
4) Use the commandline to flash Arduino boards
The main point of Arduino is that it comes with a toolchain that works mostly out of the box.
I prefer to use the command line, Kate and an AVRispmkII. This implies that I can work with any kind of AVR target
I will only use the IDE if I need some very quick very simple thing that is already available as an example sketch. Otherwise I stick to the commandline.
So once you break out of the Arduino box the money for the boards is not wasted. They are still AVR protoboards.
Having said that: I prefer the boarduino.