well, I only had to edit the config file because I had to add a certain programmer type. (I think that it's actually a big pro for avrdude, that you can do that so easily...)
the flashing parameters itself are assignable on commandline, just like with uisp! see my commands above.
I didn't look at arduinos internal IDE structure so far, So, if you aren't allready using this approach, you could invoke the whole flashing process via a makefile. Thus one could change the actuall flash procedure inside there. (I think only advanced users would want to do that anyways)
One more thing: 
I would be very happy, if the arduino IDE could be used as all full avr-gcc IDE, too.
For example, I tried to compile the ATmegaBOOT.c bootloader source inside arduino IDE and it didn't work. (it complained about the "union" statement beeing unknown etc..) I've a board with a different clock, so I had to do this. I ended up instaling the whole avr-gcc and avr-binutils by hand, which was anoying (under mac OS X) - just to compile a new bootloader.
I really like arduinos approach of doing things simple (setup(), loop() etc.), but as avr-gcc is behind it, I think it would be a big benefit to offer the wohle power inside the smart arduino IDE.
Maybe someone could document the way arduino/wiring works. So far I think of it like a wrapper for avr-gcc, but I'd like to have more insight or some tips where to look at and start to understand the backend. (e.g. im still wondering how I could add a real library)
Ciao,
Oli