When I need to drill for pins from both sides, I just stagger the holes a bit so they don't line up. Elevation is the same, but distance from FF to hole is different. Say , back 1 1/4 on one side, 1 3/4 on the other, same with the back ones. No one will know but you.
As for making one long cabinet rather than screwing together 2 smaller ones, I like one longer one. Big shops do things in increments so they need standard sizes, but smaller custom operations (me) can make any size we want, limited by plywood length somewhat. I rethink this a bit now as I'm getting old and lifting is becoming an issue, but if I can find someone to help carry it into the house, I'll make an 8' base cabinet, no seams in FF, easy install.
Good luck with your project