Can Arduino Uno, loaded with Arduino ISP, be used directly by avrdude to program an Atmega128?
Yes, that should work.
The MEGA bootloader implements STK500v2, and is located in \hardware\arduino\bootloaders\stk500v2
or the more recent version at GitHub - msproul/Arduino-stk500v2-bootloader: STk500v2 bootloader for AVR 2560 and otherchips
It does claim to support the ATmega128 as well as a number of other "larger" ATmega chips.