Because you wind up getting more total ΔV out of the deal, which is what matters. By reserving some propellant in the center core when the outer cores stage, you suddenly get a lot more ΔV out of that remaining propellant because you're not pushing as much mass uphill.
The Falcon upper stage is relatively wimpy when it comes to ΔV (it's why an Atlas can put a heavier payload into GTO/GEO than F9, even though the situation is reversed for LEO), so you want to maximize the ΔV you get out of the booster.
Edit
Tsiolkovsky ideal rocket equation1:
$$\Delta V = \ln{\left(\frac{Mass_{initial}}{Mass_{final}}\right)} I_{sp} g$$
To compute the total ΔV for a multi-stage rocket, compute the ΔV for each stage separately and sum the results.
Per Spaceflight 101, F9 dry mass is ~25,600 kg and prop mass is ~395,700 kg, and the M1D specific impulse at sea level is ~282 s (those numbers are out of date with respect to the latest Falcon cores and don't account for additional dry mass of the FH center core, but should be good enough to illustrate the point). We'll also use their numbers for the upper stage - assuming a 2000 kg payload, that should come out to 98,570 kg. And the ideal rocket equation doesn't take losses from aero or gravity drag into account, so these numbers won't reflect actual performance, but again, this is mostly for illustration purposes.
So we have two scenarios. In the first scenario, we burn all three first stage cores to depletion and drop them all at the same time:
Burn # Start Mass (kg) End Mass (kg) Delta V (m/s)
------ --------- -------- -------
1 1362470 175370 5666
In the second scenario, we burn the center core at 80%, such that when the outer cores are depleted, there's still 20% propellant left in the center core. We drop the outer cores and keep burning the remaining propellant in the center core:
Burn # Start Mass (kg) End Mass (kg) Delta V (m/s)
------ --------- -------- -------
1 1362470 254510 4637
2 203310 124170 1363
Giving us a total ΔV of (very) roughly 6000 m/s. So by throttling back the center core by 20%, we gain an additional 340 or so m/s ΔV.
- Does not take aerodynamic drag or gravity losses into account