Maybe because the Clipper is shiny and driven by people with too much money, and the Python is driven by old men in cardigans. You know what mechanics are like, they saw you coming !
(I own a Clipper, have no money, and like cardigans)
Ah, din't read.
Should be mentioned: faction reputation affects repair price.
It might seem strange, but actually it makes a lot of sense.
The Python is a pretty standardised common ship, so it's likely that most stations have spare parts, and given it's fairly generic design it's hull plating is likely very easy to replicate on-site. It's also a medium-sized vessel.
By comparison, the Imperial Clipper is not only bigger, but incredibly rare. That means spares are likely hard to come by. As if that isn't already enough to push the maintenance costs up, it has a completely custom built hull that is likely very complex and difficult to replicate (read; 3d print) on-site.
In other words, the Python is a pretty generic production ship as where the Clipper is as close to hand-built as a space craft is ever likely to achieve in 3300.
You see that 932k repair bill? That is a PYTHON. please read the entire thread. There is no special integrity repair on the Clipper, it comes from the expensive A outfittings.
As Derath clearly states here, his combat Python is more expensive on Integrity than my Combat Clipper. So that's not it. It is in fact that outfittings drive up the price of the ship integrity.
How to keep integrity damage costs down:
1. Sell everything
2. switch to another ship
3. switch back
4. Repair Integrity
5. Buy back everything