not sure there is much you can do to mask the difference in the wood. what was the original finish?
I work with alder a LOT, and one thing I can assure you of, is that when you oil it, all the variations will be highlighted, including the obvious variation between the two pieces of wood. Oil on alder looks great, the grain really stands out, and it is such a varied grain that I think it looks fantastic
Below is a picture of my dining table... alder and walnut. This has BLO and then a varnish top coat. I just ran with the differences with each board that made up the slab (as has been suggested already). The second picture shows alder using dye to change the color. You can still see the differences in the various boards, and this alder was much more "clear" than that used on the dining table. It is also BLO, but with a water based lacquer topcoat
I guess the point I'm trying to make is that it would take a seriously skilled finisher to shade and tone the two pieces so that they looked the same. rather than try to hide it, as suggested, you should consider highlighting it.
the seams in the three piece desk above were highlighted by adding a router bead down them... rather than make it look like there weren't seams, I just highlighted the seam and frankly I think that ended up looking better.