I am having the same issue... package a map through the arcmap interface, I get a file size of around 109 MB, then when I run my python script, the package becomes ~327 MB.
I did some testing with different parameters, but the results remain the same.
This was the original line:
arcpy.PackageMap_management(PublishedModel_mxd, PublishedModel_mpk, "PRESERVE", "CONVERT_ARCSDE", "DEFAULT", "ALL", "DESKTOP", "REFERENCED", "ALL", "", "", "")
and I also tested the code with switching around the Convert_data parameter, the convert_arcsde_data parameter and the reference_all_data parameter.
UPDATE:
After some testing, I think the issue was with the version parameter. Choosing the versions Current (10.8), 10.6 and 10.5 versions together got my map package to the same size as the map package from the manual tool.
The default from the model seems to be ALL versions, and that is different from the default manual interface option.