Re: installing new inlays on an existing fretboard
For dots, you can just drill a hole to size of the dot you have and glue the dot in (or just fill the newly drilled hole with clay or something like that). This you can do without a refret and you'll just have to sand the inlay flush to the fretboard.
Now if you want a design like trapezoids, blocks, celtic crosses etc, you will need to level the fretboard entirely (meaning a refret later), cut out what you want, insert the inlay, radius the board, fret it, and then all the setup work ensues.
For some guitars, I would rather just make a new fretboard starting from there, removing the old fretboard carefully with a heat gun (or moisture if the glue is water-soluble) and gluing the new fretboard on. I think this would be better in the case of a set neck guitar like a Les Paul where material is removed from the fretboard - therefore the frets will be positioned lower which could be problematic during setup in relation to the bridge. On bolt-ons you would be able to just shim the neck to the correct height.