You can zero the irons on an M249 or M249S by setting the elevation to 700m and zeroing at 10m, or by setting the elevation to 300m and zeroing at 25m.

What is your preference and why?

Short distance zeroing is meant to only be used when a longer range is not available.

It is ideal to zero at the longest distance available.

Of course.  But most folks do a short distance one first to save range time and ammo.  I get virtually unlimited 10m and 25m range time, but can't say that for real distances.

FPNI...…..

He said, ".....It is ideal to zero at the longest distance available...……."

If that's 25m, then 25m it is.  
If it's 100yds, do that...……

But if you are going to get all technical/Military 25 meters is not 25yds and 100yds is not 100 meters.
So get your range finder out and have fun converting...…..

Everywhere I shoot is in real meters except for one fudd range.

I agree that longer is always better- as long as the 25/300 trajectory match is spot on, or at least as close as the 10/700 one.  And that is something I do not know for a fact, since all of the mil zeros I've ever done were using the 10/700 even though 25m range abound.

That will make it easy.  
Interesting, except for the pop up and a few KD zero ranges on military bases I've been on the rest of the ranges have been in yards.
Various Army and Marine (Quantico and Pendleton) all have been in yards and all civilian ranges.

But hey that makes your zeroing easy...…………..  but then you'll have the opposite, if you end up shooting on a civilian range to confirm zero's you'll need to convert.

You asked why? as a second part of your question.  The further out you can zero means the zero will be more accurate further out.  
Just my humble experience is that the zero's on the LMG's (M240 and M249) were at best simply a estimate.  The BDC's and zero's were always off "further out."  It was better than nothing and the Army insisted on doing it that way.
With my own guns I would ALWAYS shoot to atleast 100yds (200yds mostly) to get a good zero for "further out."

Whats the sight height of the M249?

I used 2" for running this ballistic calculator.

https://bergerbullets.com/ballistics-calculator/

11yd = ~10m zero:



27yd = ~25m zero



The 25m looks way better / easier to compensate for.

thank you!