There are three achievements for each ship; you start with the TYPE A layout, and when you have completed two of the three achievements, you unlock the type TYPE B layout for that ship.
If you are trying to get the third ship achievement (just for the sake of completeness), can you use the TYPE B layout to do so, or can achievements only be won with the "default" TYPE A layout?
Ship achievements can be won using the TYPE B layout.
In addition, if you already completed a ship achievement on Easy mode, you can complete either of the two old achievements again on Normal.
Source: Testing in a personal play-through.
Here you can see the Red-Tail (the secondary layout of The Kestrel Cruiser) with only one HP remaining on the hull...
...and then earning the Tough Little Ship achievement when it is repaired.
