Since VSTEP needs permission from ship owners, who are presumably concerned with their image, re-skinning might violate their agreement with VSTEP.
On the subject of tweaking, while I think that making performance values available in an editable text file, as Trainz does, would be handy, I see one drawback from VSTEP’s and mission designers’ perspectives:
Many missions depend upon the vessels having certain performance, such as max speed.
For instance, a mission that depends upon one ship overtaking another within a set time might fail for players that have tweaked their vessels.