Well, pilsner extract IS "LME."
"LME" is just a reference to liquid malt extract, which can be made from different types of base grains. A standard light/extra-light LME is usually made from a regular domestic 2-row malt. A Pilsner extract (also LME) is made using Pilsner malt as its base.
Pilsner malt is usually a little lighter in color and has a slightly different flavor than regular domestic 2-row, and actually in this case will get you a little closer to the style. Most Belgian ales start with a Pilsner malt as their base grain, so you're actually probably going to be a little closer to accurate.
In the end, though, the differences are very subtle. The beer will be good. RDWHAHB.