What is legacy joinery? trying to use existing mortices? It may be possible every now and then, but the new structure will be a very different design.
I plan to compensate for the morticed areas of the beam by upsizing the beam size to compensate. I had the plugging in mind for looks and maybe to get a small percentage of the strength back (in compression).
And I am an engineer (ME). I'll be refreshing myself in truss/statics loading analysis and stress analysis. I'll also definitely have my worked checked by another professional with this type of experience. The more cross checks the better. Being able to do much of the calculations myself will allow me to experiment with designs and get close with the minimum sizing of members.