Assuming A) space vessels and

civilian ships
not designed with the worry of being shot at (as opposed to accidents happening):
A civilian ship (if its designed by smart people interested in maximum cost efficiency) will have their life-support spaces (places where people can live) made airtight against possible leaks. A military vessel will have their life support spaces divided up too, but instead of just sealing them off they will actually armor
inside the ship where they are sealing off. Weapons grade lasers and the like don't just
melt or (in the case of railguns) smash their way into the ship; razor sharp hyper-velocity fragments (i. e. take your hand off if its in the way, even if the splinter isn't actually sharp) will be sent flying all over the place.
A civilian vessel will place critical systems -- hull, drive, probably life support spaces as well -- near the "skin" of the ship, for easy access and repair in case of accident / needed maintenance. A military vessel will put those wherever they can be the best protected, even if thats in the center of the ship where repair / replacement will be very difficult / impossible, because that increases the chance of the ship coming home.
A civilian vessel will have backups for critical systems, yes. But it won't use
multiply redundant systems, designed to operate completely independently while also being cross linked (e. g. you may have several different drive control systems, all with independent control runs, but the runs will be cross-connected so you can route around damaged sections through the runs for the other (possibly disabled) systems). A smart military designer would do that, if possible.
A civilian ship won't be very heavily armored -- any armor it might have would be focused against micrometeorite degradation. Need I explain why a military ship would do things differently? (Or that you can't simply slap armor onto something that wasn't designed for it?)
America's civilian factories were sitting idle and in disrepair. Within 90 days the car factories were producing trucks, the tractor factories were producing tanks and aircraft, ports were producing warships in less than 9 months.
Let me just point out that its quite possible to
retool a factory to build something other than what it was originally meant to build (especially when the items in question are related). That doesn't change the fact that they are completely different items.
Lets also take, as an example, the idea of a gaming computer Vs. a "plain" desktop computer, such as released by Dell or Gateway.
Gaming computer would have a highly powerful CPU; desktop computer would have something "strong enough" for word processing, running windows, and browsing the internet. Sure, there will be a quite a bit of overhead in that, because adding in that extra speed is cheap compared to the marketing advantage you get from it.
Strong GPU would be faced by -- quite possibly -- not even having a GPU slot.
A strong, capable motherboard on the one side, would be faced by a motherboard thats "just good enough" -- low memory speed, a few PCI slots, probably not any PCI-E or AGP slots (though some of the higher end ones do have those, most of the low end ones using an integrated video chip don't bother installing a PCI-E slot even if the board can use one).
Lots of fast memory Vs, again, memory "just good enough" -- slow, and probably not much of it since you can cache off the disk drive.
Even if you wanted to upgrade the desktop ("civilian") computer to a gaming ("military) one, you can't -- not without replacing just about everything from the motherboard up. Depending on the company, you might even have to replace the case -- I've heard of companies that use proprietary designs for their cases and motherboards, so they aren't interchangeable with their own hardware (i. e. their own desktop Vs. gaming motherboard either won't fit on the same screws, or the same backing, etc etc), much less external hardware.