Lets do a loopback test for SPI, so short MISO to MOSI and power VCC with 5V.

sudo usermod -a -G spi rsutherland
mkdir spiLoopBack
cd spiLoopBack
wget https://raw.githubusercontent.com/epccs/RPUno/master/SpiSlv/spidev_test.c
gcc -o spidev_test spidev_test.c
./spidev_test -s 1000 -D /dev/spidev0.0
./spidev_test -s 10000 -D /dev/spidev0.0
./spidev_test -s 100000 -D /dev/spidev0.0
./spidev_test -s 250000 -D /dev/spidev0.0
./spidev_test -s 500000 -D /dev/spidev0.0
./spidev_test -s 1000000 -D /dev/spidev0.0
./spidev_test -s 2000000 -D /dev/spidev0.0

The test output

spi mode: 0
bits per word: 8
max speed: 500000 Hz (500 KHz)

00 00 00 00 00 00
00 00 00 00 00 00
00 00 00 00 00 00
00 00 00 00 00 00
00 00 00 00 00 00
00 00 00 00 00 00
00 00

Those should not be zeros. I connected the R-Pi to node MIS0 (note the zero) and the buffer to MISO. After some rework it is passing the loopback test.

spi mode: 0
bits per word: 8
max speed: 500000 Hz (500 KHz)

FF FF FF FF FF FF
40 00 00 00 00 95
FF FF FF FF FF FF
FF FF FF FF FF FF
FF FF FF FF FF FF
DE AD BE EF BA AD
F0 0D

Next I have added a linuxspi rule in the RPUpi Remote application's Makefile. I used sudo because of an issue with permissions.

linuxspi:
	sudo avrdude -v -p $(MCU) -C +$(LIBDIR)/avrdude/328pb.conf -c linuxspi -P /dev/spidev0.0 -e -U flash:w:$(TARGET).hex -U lock:w:0xef:m

Ran this icsp.py script on the working folder with that Makefile.

https://github.com/epccs/Driver/tree/master/ICSP/Icsp

python ~/bin/icsp.py
rsutherland dialout gpio spi
rsutherland dialout gpio spi
sudo avrdude -v -p atmega328pb -C +../lib/avrdude/328pb.conf -c linuxspi -P /dev/spidev0.0 -e -U flash:w:Remote.hex -U lock:w:0xef:m

avrdude: Version 6.3-20171130         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/         Copyright (c) 2007-2014 Joerg Wunsch
         System wide configuration file is "/etc/avrdude.conf"         User configuration file is "/root/.avrduderc"         User configuration file does not exist or is not a regular file, skipping         Additional configuration file is "../lib/avrdude/328pb.conf"
avrdude: warning at ../lib/avrdude/328pb.conf:4: part m328pb overwrites previous definition /etc/avrdude.conf:8573.
         Using Port                    : /dev/spidev0.0         Using Programmer              : linuxspi         AVR Part                      : ATmega328PB         Chip Erase delay              : 9000 us         PAGEL                         : PD7         BS2                           : PC2         RESET disposition             : dedicated         RETRY pulse                   : SCK         serial program mode           : yes         parallel program mode         : yes         Timeout                       : 200         StabDelay                     : 100         CmdexeDelay                   : 25         SyncLoops                     : 32         ByteDelay                     : 0         PollIndex                     : 3         PollValue                     : 0x53         Memory Detail                 :
                                  Block Poll               Page                       Polled           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------           eeprom        65    20     4    0 no       1024    4      0  3600  3600 0xff 0xff           flash         65     6   128    0 yes     32768  128    256  4500  4500 0xff 0xff           lfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00           hfuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00           lock           0     0     0    0 no          1    0      0  4500  4500 0x00 0x00           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00           efuse          0     0     0    0 no          1    0      0  4500  4500 0x00 0x00
         Programmer Type : linuxspi         Description     : Use Linux SPI device in /dev/spidev*

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x1e9516 (probably m328pb)
avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as D6
avrdude: safemode: efuse reads as FD
avrdude: erasing chip
avrdude: reading input file "Remote.hex"
avrdude: input file Remote.hex auto detected as Intel Hex
avrdude: writing flash (5792 bytes):

Writing | ################################################## | 100% 1.60s

avrdude: 5792 bytes of flash written
avrdude: verifying flash memory against Remote.hex:
avrdude: load data flash data from input file Remote.hex:
avrdude: input file Remote.hex auto detected as Intel Hex
avrdude: input file Remote.hex contains 5792 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 1.34s

avrdude: verifying ...
avrdude: 5792 bytes of flash verified
avrdude: reading input file "0xef"
avrdude: writing lock (1 bytes):

Writing | ################################################## | 100% 0.01s

avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0xef:
avrdude: load data lock data from input file 0xef:
avrdude: input file 0xef contains 1 bytes
avrdude: reading on-chip lock data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 1 bytes of lock verified

avrdude: safemode: lfuse reads as FF
avrdude: safemode: hfuse reads as D6
avrdude: safemode: efuse reads as FD
avrdude: safemode: Fuses OK (E:FD, H:D6, L:FF)

avrdude done.  Thank you.

icsp_pin falling event occured so use_bootload_pin_to_stop flag cleared
press icsp_pin again to end program

That was fast, that was the fastest I have seen anything go.