Seconded, I deploy large packages with gigabytes of deep learning and GIS dependencies in single executables with Nuitka and it works very well. Also handles including data files into the executable if needed.
Out of curiosity, are the GIS dependencies the proprietary ones (coughESRIcough)?
Ha ing been down a similar path, this whole thing works so much better if you don't 'import arcpy'. Licencing issues aside, you've often got faster tools in shapely, fiona, geopandas, rasterio, xarray.
Please no, not ArcGIS. I’m sure our dependencies would clash with arcpy’s if we tried. Fortunately my company uses FOSS packages almost exclusively.