Alright,
So I've seen some pretty good prices on some new Howa 1500s that come with 16" threaded barrels.  Don't ask me why, but for whatever reason, I've really been jonesing for a short bolt action.  My question is; does one caliber have a more significant velocity loss out of a short barrel than the other?  Then again, being in the DC area, it's not like I have much of a range to shoot at anyway

Rule of thumb is that heavier, lower pressure, and larger calibers experience less velocity loss to reduced barrel length than lighter higher pressure smaller calibers.

.308 is already a good (possibly better) choice for shooting out to intermediate ranges (<400yds or so) where it delivers more energy and windage is still somewhat trivial. Beyond that the ballistics and windage of the 6.5 start to catch up and ends up being better at everything.

If I were going to go with a “shorter” precision rig I’d keep it in .308 if my intended targets were <400yds versus the 6.5CM.

Sounds like it won't matter. Just buy whichever one you are already shooting or are setup for. If I had neither I would go 6.5 Creedmoor so that if you ever wanted to build a longer range gun you would already be setup for it.

I had a 26" 1:8 Criterion Rem-Age 6.5 Creedmoor; I got 2820 with a 140gr HPBT over 42.5gr H4350 and 2857fps with 140gr Amax Match factory ammo (barrel had about 950rds through it).

Same barrel cut back to 18" got 2640fps with the 140gr HPBT load and 2662fps with the 140gr Amax Match factory load.

I now have a 18" 6.5 Creedmoor PVA/Rock Creek which gets 2540fps with 140gr ELD-M factory ammo (these have always been a bit slower than Amax match in my experience) and Berger 135gr Classic Hunter runs about 2565fps.  That barrel has about 200rd on it where the Criterion was north of 1000, but I dunno if it'll pick up any more speed at this point.

I don’t have any experience with the 6.5 CR, but generally you loose about 25 fps with every inch of barrel that it is shortened. Most 308 test barrels are about 24 inches where the 6.5 CR has a 26 inch barrel. Which mean the 6.5CR velocity is going to be effected more with a shorter barrel.

I maybe old school but if it were me, I would take a 308 especially if your not shooting past say 500 yards.

I am having the same internal debate. The SIG Cross is appealing to me in very naughty ways and I was having trouble figuring out if I should go 308 at 16" or 6.5 at 18". I think I will stick to 308 since I have thousands of brass and bullets with usable powders in my reloading room. I already get crazy good velocities out of my current 18" 308. My 165 Speer lodas get 2650 with a mild load and my 178 ELD-X load gets 2620 from the same barrel with a mild load.

Don't know about the Sig, but for (what I would imagine) the same cost or less, Eurooptic has the Tikka TacA1 in .308 with a 16" barrel for $1600 and change