You mean it is designed to have a challenging AI opponent when played with "none" bonus !!???
And I tried it with "medium"...
AFAIK, you are wrong about bonus effect on ship building : "bonus" multiplies production, research AND construction rate by a factor of 2(low), 3(medium) and 5(high).
Even if AI homeworld build cheap ships one per turn, what about base space yards ? The also receive construction bonuses.