G'day, JD. I feel your pain, but I am not 100% clear on your problem! Is it that the cut-out and finished coaming will somehow overlap (viewed from above) part of the deck beam (or in other words, part of the deck beam will be revealed)?
If 'yes' to the above, presumably it is only a curved portion at the very front of the cockpit, and you are thinking of maybe routering away that portion of deckbeam that is visible.
I wouldn't (unless it's only a few mills), and if I did I'd use a half-round file rather than a router - tricky things! Why not take the reverse approach by adding a layer or two of material - as many as needed - (3mm ply will bend easily enough) around the front vertical edge of the inside of the coaming so that eventually the deck-beam is completely underneath this added material, again as viewed from above. If you taper or feather the added material back as it reaches the ends of the covered part it will blend in more, too.
Or, if you are painting the coaming (as I do), you could simply fill the front part described above with thickened epoxy to cover the exposed section of deck beam and sand back when cured.
A third, quicker-and-easier alternative, might be to cut out a strip of 1" MiniCell foam and stick this around the front internal edge of the coaming, also giving you some 'bump protection' as well as disguising the exposed part of the beam.
Not the end of the world - we've all been there, done that! And as I read elsewhere - "I measured it three times and it's still too short"!!!
Enjoy the rest of the build.
Wordsmith