The glue won't darken at all.
Try filling a scrap piece of wood similar to what you are trying to fill
and (after it dries) wipe it down with a bit of liquid drain cleaner...or
better yet a bit of lye in some water. That should show you what it will
eventually look like if you are planning on letting it age naturally.
I've not had too much success with the technique you are describing.
About the best thing I've found is a wax pencil over the first coat or
two of finish.
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