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Yes you can. However, with some woods, the slight color variation between the filler and the real wood may become more apparent, while with others, oil finishes tend to even out things.
I don't know...

You can mix very fine sanding dust (from the wood you used) with normal PVA glue (white wood glue). Mix it with a scraper till you get a very fine, even-colored paste. It's a fairly invisible filler....