[Fyron]

Supplies and maintenance are entirely different aspects. Maintenance is resources paid per turn. Supplies allow your ship to move, power shields, and fire weapons. Running out of supplies drops your ship's movement to 1 [corrected] and prevents it from firing weapons. Its shields will be at 0 at the start of new battles where the supplies were 0.

If there was an advanced trait for maintenance reduction (I believe one could be modded in), it would add linearly just like the characteristic and cultural bonus do. Traits and culture affect the base maintenance rate, not the maintenance paid. If it was at 25%, it would make the base maintenance rate 0%. The 5% minimum rule would then apply.

It is possible to modify the system so that maintenance traits and cultural bonuses seemingly affect the actual maintenance paid, which is a far more logical and balanced mechanism. It involves setting the base rate to 100 in Settings.txt and adding a -75% maintenance reduction ability to all ship hulls (change the one on base hulls to -90%). Without any bonuses, ships will still have an effective maintenance rate of 25% (0.25), as in the stock game. Selecting a maintenance aptitude trait of 110 will cause the maintenance of a ship to equal to:

(base - trait) * (base - maint_redux_ability) =
(1.00 - 0.10) * (1.00 - 0.75) = 0.225 of the build cost

This is a 10% reduction of actual maintenace paid, rather than the base. In stock, a 110 value in that trait leads to a 15% base maintenance, which is a massive 40% reduction. Of course, you will want to fiddle with the threshhold costs of Maintenance Aptitude, as it will become way too expensive for what it does past 110.

Ashton:
The Space Monsters of Devnull have negative maintenance rates, representing hording factors.