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I will be fretting my neck today. It has a bolt-on mortise and tenon neck joint. I've read that it is best to add the frets to the section of the fretboard that sits atop the soundboard when the neck is mounted to the guitar. I realize with a dovetail joint that this makes sense. But is there any reason why I shouldn't install the frets with the neck off the body in this case since it's so easy to re-attach the neck? I know this may seem obvious, but I don't want to screw it up at this late stage. Thanks!

There's a variety of sequences to accomplish that task, and each has pros and cons.
I install frets before I glue the board to the neck, one reason is the difficulties of fretting after the board is on the neck.
I would fret at least the extension before installing the neck, probably the whole board.
You do need to wait until the neck is installed to do final leveling and dressing.

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Thanks Rodger. Being that it's a bolt-on, I should be able to dress the frets off the guitar, no? Also, I've been wondering if I should hot hide glue the fretboard that sits on the soundboard when all the leveling and dressing is done. Thanks for your help.

You can fret the board with the neck off of the guitar, but you will want to level and dress the frets after the neck is attached and the extension is glued to the body. When leveling and dressing frets you should be removing relatively small amounts of material and only in the places it needs to be removed. If you are talking about filing fret ends, that can be done prior to attaching the neck, and is easier to do then.

I level the fretboard after I glue it down to even out any minor irregularities, then fret the whole neck.

I use bolt necks as well.

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