I had that same frustration this week. Trying to generate geotiffs from arrays in Python. I found four libraries, all of which just wrap GDAL, all of which have the same quirky issues. Alas. :)
I wish I was smarter and could debug further. Issue doesn't happen standalone but happens in a qt5 plugin for GDAL. I was hoping to find any other implementation of array to tiff in order to avoid this crash. Alas.
We heavily use GDAL/rasterio/numpy at work with no real problems.