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I recently bought an ebony fingerboard from LMI and had them slot it for me. I expected that the slot for the 1st fret would be the proper distance from the flat/nut end of the fingerboard. Instead the board came with an additional zero fret slot. I'm thinking that if I simply cut the end of the board at the edge of the zero slot, the 1st fret slot will be too close to the end of the fingerboard since the slots are dimensioned center to center. If I cut the edge of the fingerboard at the center of the zero slot, the 1st fret will be the proper distance from the end of the fingerboard but I will have a rabbet on the nut end of the fingerboard. Or am I missing something here?

What scale is the board? If it's 25.5" (Fender scale) they usually leave some wood behind the nut, ala Fender. I'm not certain if they cut the nut slot 1/8" wide, or simply cut a slot at that location the same size as the other fret slots. This could be what you're seeing. What you see as a zero fret slot would actually be the where the face of the nut goes. I can't imagine they'd cut a slot for a zero fret unless you specified it.

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Mike

The only thing nescessary for evil to thrive is for good men to do nothing.

It will be fine if you just cut it off
Many luthiers shorten the nut to first fret distance deliberately to improve inotatation.

"The nut position is marked by an additional slot (sometimes called a “zero” fret) – just cut off the excess fingerboard wood at this slot." this is right off the LMII site under shop services, My advise would be measure from the center of the 1st fret to the end of the zero fret location where the face of the Nut would be, If that measures out to the correct first fret distance in your scale length your all set. If the distance is too long take a little off the end of the board till its accurate if its to short fill the fret slot then cut it off to the proper length.

I always just cut the fretboard off right there. I've never had any intonation problems from that.

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Old growth, shmold growth!

You can always shape your nut to add back that extra ~.01" if needed. I actually prefer to cut the fingerboard 1/16" ahead of the zero fret to give some space for compensation ramps filed into the nut as well as the saddle. Like Jeff said, more intonation control. Nut compensation allows changing the length of open strings without affecting fretted notes (a good thing, since the amount of sharpening due to stretching down to the frets is not necessarily equal across all strings).

The nut is frequently moved about .01-.015" toward the bridge on many high dollar electrics.
Made a whole lot of em over the years. I can't recall the builders names but there were quite a few that always specified this feature.

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How long is that in luthyears?