Hi there
I had the same issue with a carved top LPS earlier this year. Some people can live with the gap, some (including me) would prefer not to have it.
Options include filling the gap or lowering the neck. I chose to lower the neck by increasing the depth of the neck pocket. I actually took a little too much out and had to rebuild it with an epoxy/wood dust mixture. The end result was well worth the effort and I wouldn't hesitate to do it again.
A couple of things to take into account:
You will need to use shorter screws to attach the neck.
You can adjust the neck angle at this point to suit your bridge selection, playing comfort, etc.
Be aware that neck pocket adjustment is not a trivial exercise and it may well be worth taking to a luthier.
There is also a mindset issue. The parts do not constitute a "kit", ready for assembly. Rather, they are a basis for you to achieve a personal result, ie. a shortcut to having your own custom made guitar. In some cases, very little modification may be needed, in others it may be more extensive, depending on what you want out of it in the end.
That said, I have to admit to being surprised by the fretboard gap when I first encountered it as well. A deeper neck pocket option would be nice to have for carved-top guitars and others that are not going to have a scratchplate. I don't know how difficult this is to implement, but it may be worth some consideration.
Hope this helps.