Programming an atmega328p via raspberry pi gpio and avrdude incompatible with logic level shifter?

30 euros/dollars for a LHT00SU1
It is a Logic Analyzer plus one analog channel.
Software : sigrok / PulseView and a tool "Zadig" is needed in Windows.
Turn off the analog channel to be able to sample the digital inputs at a high rate.

There are already 10k pullup resistors on the low side and 10k pullup resistors at the high side. You can add an extra 4k7 pullup on high side and 4k7 pullup on the low side.
However, I prefer that you buy normal digital level shifters. Not that bi-directional I2C rubbish.