The biggest thing that has worked for me is to preempt interruptions by giving him quality attention at mealtimes and during times when I "come up for air" between deep dives. I also make a point to get up from the chair periodically, and I take those times to give him a pat on the shoulder or a hug or something.
To a kid deep concentration can look a lot like anger. I make a point to respond to him in some fashion whenever he reaches out - give him a hug or something emotional and nonverbal. A lot of these interactions are just to show him that I'm there, I'm not angry. This low-level emotional stuff usually doesn't take me out of my front-brain programming head-space.
I used to worry that I wasn't always having "real" conversions with him. He'd jabber about whatever and I'd give "uh-huh" and "that's cool" answers. But I realized a lot of that is what linguists call phatic communication. What he seems to want from those conversations was a sense of connection rather than actual deep conversation. It would be a problem if we never connected, but as long as we had some quality time it seems okay if some of our conversations are on "autopilot".
I also talk about my work with him. For me it's like having a "rubber ducky" convo and he tells me it sounds like Star Trek technobabble. It gives him a sense that I'm doing complicated things inside my head but I still care about him.