Some debugging is needed from your side to understand what is going on.
Like this other issue with the Python engine, my guess is that the trouble lies in casting data from Python to Matlab.
As sanity check, create a Matlab function pipeline_test.m that does what you need:
% Process: Create link to raw files
sFiles = bst_process('CallProcess', 'process_import_data_raw', [], [], ...
...
...
...);
% Process: Import MEG/EEG: Events
sFilesEpochs = bst_process('CallProcess', 'process_import_data_event', sFiles, [], ...
...
...
...);
% Process: Average
sFilesAvg = bst_process('CallProcess', 'process_average', sFilesEpochs, [], ...
...
...
...);
% Print outcome
sFilesAvg
and call with a simple Python script
import matlab.engine
eng = matlab.engine.start_matlab()
res = eng.pipeline_test()
print(res)
If this works as expected the issue is indeed how the arguments for the processes are passed from Python to Matlab. E.g., try to pass all numeric data as float
Also, you can redirect the standard output and standard error, to verify is an error was raised in Matlab: