Is it better to have a bolt sticking out than not?

I see that most bolts are made long enough to stick out over the rails, I can see that this is needed if your bolts have broadheads that might not sit well on the rail, but what if you're using flushed points?

Is there any performance advantage to the bolt sticking out rather than not?

The length of the bolt is not really important (neglecting FOC at this point).

If your bolt lies savely in the groove or the rest everything is fine.

Needless to say a bolt sticking out too long is some kind of inconvenient.

A bolt that is very(!) short is usually coming with disadvantages in balance point inflecting flight dynamics.


Relating to medieval, bolts were usually categorized (incidently read about it in "Die Armbrust" yesterday) by the type of Crossbow ("Halbe Ruestung" for example to be about 2.47oz (~1/45 of bow weight) and 15.35 inches ) with little or no adjustment to the weapon.

When considering making long and narrow bolts compareable with bow arrows a thing comes to a point usually not wished with crossbows: spine and archers paradox.
A long narrow bolt will bend during acceleration, a stout one would not be influenced by that so dramatically. But this phenomena inflicts bolt flight a lot and with high power weapons bolt breakage is more likely to occur.


In conclusion: If you make your bolt with little differences to your rest you would do fine without running into trouble.

Rizzar

From my personal experience I've found that bolts the same lenght as the bolt track they are fired from, or just a bit longer if a broadhead or other larger-than-shaft diameter point is used, fly truest. I've tried longer bolts or arrows experimentally, and there is always more wobble and other eccentric behavior. I have not tried ultra short bolts.
Gnome

The geezer's eye view of long vs short bolts.
Short bolts have less surface friction for their mass, so they go a little faster over longer distances, but they also go deeper in your target and hence tend to shed their fletching.  They're more compact and use less arrow-shaft.  I used to make 10.5 inch bolts as my standard because I could get three per cedar arrow-shaft. 
My target-shooting customers often swear by longer bolts-16 inches or better, for stability... which might be true if the balance is right.  Using standard weight field-points, you can run into problems with insufficient head-weight for the shaft.
Longer bolts stick further out of your target, so they don't shed feathers as readily, but long, whippy bolts can fail under acceleration or on striking the target obliquely.
Medieval illustrations often show bolts protruding over the front by several inches, so they had to deal with the same question... extant medieval bolts run anywhere from 12 to 18 inches in length, but the average seems to be about 15 inches (38 cm) Given short draw and relatively high brace-height of many medieval and renaissance bows... say 5-6 inches of draw from 4 inches of brace, plus an inch or so extra ahead of the prod, we get maybe 11 inches from front of prod to the lock, for a 4 inch overhang.  And yeah, that's pretty much consistent with drawings/paintings.  So by medieval standards, a fair overhang should be no big problem.  Geezer

Great stuff Geezer, didn't think about the bolt burying itself . I was actually looking to see how short of a bolt I can use, related to an autoloading system I'm trying to iron out. I remember reading somewhere that fin-stabilized kinetic penetrators (basically a cross bolt right?) have an optimal flight dimension of 20:1 length/diameter ratio.

Not sure how well that would apply for the crossbow bolt, but with a 1/2 inch diameter shaft, that would make 10 inch as the optimal length.

I guess the only way to know for sure is to experiment.