Out of curiosity, I did a similar comparison but flipped the build costs.
Cost to build (in PlanetImprovements.xml):
Traditional Factory = 150
Xeno Factory = 125
Advanced Factory = 100
Manufacturing Center = 175
Industrial Sector = 50
Cost to purchase:
Traditional Factory = 1482
Xeno Factory = 1212
Advanced Factory = 948
Manufacturing Center = 690
Industrial Sector = 438
Cost to upgrade from Traditional Factory:
Xeno Factory = 438
Advanced Factory = 438
Manufacturing Center = 438
Industrial Sector = 438
Cost to upgrade from Xeno Factory:
Advanced Factory = 336
Manufacturing Center = 108
Industrial Sector = 438
Cost to upgrade from Advanced Factory:
Manufacturing Center = 72
Industrial Sector = 438
Cost to upgrade from Manufacturing Center:
Industrial Sector = 438
Odd result, it would cost LESS to go XF->MC->IS or AF->MC->IS than XF->IS or AF->IS (with my new prices). It seems like if the upgrade difference is below a certain amount, or negative, it defaults to a build cost of 50 (purchase cost of 438).
Nonetheless, I'm glad to see lower build/purchase costs for upgrades.