So, you are about to string up your first guitar build! This is a very exciting experience. Congratulations! On your first build there is a fairly high chance that you will end up doing some adjusting of that neck joint in the first few weeks after you string it up. That is OK - it is one of the great advantges of a bolt-on design that you can do that easily. For this reason I suggest that leave the fingerboard extension unglued initially so that you can get the neck on and off without further bother. BTW, you don't even need to remove the string when you are taking the neck off. Just loosen them but leave them attached at the headstock and hold them in place on the neck by putting a capo on (I put two capos, one at 2nd fret and another at about the 9th) - then take out the bridge pins and detach he strings, but leave them on the neck. You can reattach the strings in a jiffy once the neck is back on (but, of course, this trick doesn't work for a classical or pinless bridge).
The guitar can live with the fingerboard extension just sitting on the soundbord, unttached, until you are happy with the setup. But sometimes this can be a source of buzzing as the two sufaces vibrate without being coupled together. So, once you have your neck all sorted out you should probably glue the FB extension down. You are right to say that this can be a very weak glue joint, to assist future disassembly. So just a thin smear or a few dots of some sort of weak wood glue that will easily release later with a bit of heat.
Recently I have been building with a bolt-on and bolt-down design, so there is no glue at all. The Gore & Gilet books outline a method for this. I have used this system and really like it:
http://www.luthierscooltools.com/Tools.htm#Bolt-on
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Check Ch. 15, Step 8, Pinning the Neck. in my book, it's on page 336. They mention a "fine bead along the edges of the heel where they contact the soundbox." Done for appearance sake, as I take it. Just wondered if anyone did this.
