Surprisingly the upgrade of the stronger V2-CTR Miner is cheaper than the of the SCL1-R.
Miner installation time upgrade from Level 1 to Level 2 costs
-1.4K and 150Scalar for the SCL1-R
-1.5K and only 100Scalar for the V2-CTR
It looks like a feature and i am unsure if it is wanted that way.
The other upgradecosts for installation time seem inconsequent too.
For instance Level 0 to Level 1:

• 400 + 1XP-Paper for MTRX-3
• 450 + 1XP-Paper for TN4S-R
• 400 + 1XP-Paper for IN5-AR
  It is the same for the Level 0 to Level 1 for Max upgradelevel (Order:Scalar,Vector,Matrix,Tensor,Infiar).
  1K of the according recource+ 1Blue Starpaper/1K/1K/1K/1K
  Every time it costs 1K of the recource that the miner mines. Except for the first one (SCL1-R).
  Level 0 to Level 1 mining speed:
  500/400/400/350/400 green papers
  Why does the first miner cost the most? Why is the fourth one cheaper?
  I have no access to other upgrades yet, maybe the issue exists also for higher levels of upgrades.