There are several parameters in the FTDI chip that can be tuned.
Things like the latency timer can start to be very critical when pushing up on the speeds
particularly in a request/response environment like this.
There are also similar parameters in the drivers.
The settings for "normal" situations often hurt in environments that want/need
low latency fast turn around times.
Also how the application (avrdude) does its reads/writes or the mode it puts
the tty port in can start to make a difference.
While measuring things can provide a performance snapshot,
I'm never a fan of just measuring things when looking for tweaks to performance
as it really doesn't tell enough of the picture.
The best way would be start actually profiling the the entire system (avrdude, USB bus, optiboot)
to see where the bottlenecks are because often it can be unlikely places.
--- bill