Solution has been worked out:
1) Develop in the Arduino IDE all of the programs/sketches that you will need
2) In the Arduino IDE, turn ON verbose output via File -> Preferences
3) Upload program 1
4) When upload is finished, record the last line of the compilation output. If my program is called blink1, then I saved this line to blink1_cmd.txt
Note that in the example shown, the last line is:
C:\ArduinoIDE\hardware/tools/avr/bin/avrdude -CC:\ArduinoIDE\hardware/tools/avr/etc/avrdude.conf -v -v -v -v -patmega328p -carduino -P\\.\COM9 -b115200 -D -Uflash:w:C:\Users\PAULJO~1\AppData\Local\Temp\build6145494704296263461.tmp\blink1.cpp.hex:i
5) Find the HEX file associated with your program and save it elsewhere. In the case above, the HEX file is:
C:\Users\PAULJO~1\AppData\Local\Temp\build6145494704296263461.tmp\blink1.cpp.hex
And I moved it to:
C:\Users\PAULJO~1\Documents\MATLAB\TestCode\Arduino\ArduinoIdeProgramming\blink1.cpp.hex
Please note: If you run into trouble, try using folders without spaces
6) In your text file, update the HEX file path
7) Copy the entire line from the text file
8) In the Matlab command window:
[status,cmdout] = dos(' paste code here ')
You should get an output of:
avrdude done. Thank you.
9) Repeat as necessary for the other programs.