You guys are over analyzing the situation! It totally does not matter what the reason is for a tantrum, a tantrum should never be allowed. This new dinner time drama is the perfect opportunity for you, BOTH of his parents, to set the new routine, which is a family dinner. Whatever his reason for revolt-possibly because he has everyone's undivided attention, possibly because he prefers not to change his routine-doesn't matter! He's 3, and you're the parents. You don't have to change the menu or the time or anything. All you have to do is enforce your household rules until he understands them.
Yes it's a phase. It's a phase he can outgrow on his own terms at his own pace while running the household and ruining dinners, or its a phase you can end.
Hopefully he is not allowed to have tantrums at other times, which would make it hard to control them at dinner. Whatever your most effective form of discipline is, you need to implement it immediately when he begins these tantrums, and continue the consequence until he stops. Do not let the tantrums escalate or play out. Be absolutely consistent until he learns he NEVER gets away with it, and he'll learn to come to the table and participate in dinner like a gentleman. He's not too young. The amount of time this takes depends on what type of discipline you choose and how effective it is.
Also, since he's a boy, and since his dad is there, his dad should be the primary disciplinarian in this case, and you should back him up. He may be lashing out for attention because dad showed up etc. His strongest role model is his dad, so it's his job to teach him this isn't allowed. Don't let "guilt for being gone all day" into his mind for excuses, lots of men work all day. Once this is settled, dinner will be awesome for bonding, and as you said, they play together afterwords. A bit of discipline for these tantrums is the perfect missing piece to the picture.
As a side note-this is a sleepy time of day. My daughter had a few tantrums before dinner for a while, and she is NEVER allowed to indulge in tantrums and she knows it. But she was so sleepy form waking from a late nap, it was like she couldn't help it. I did implement her consequence, but I now also make sure she is fully awake at the time we start dinner. This (discipline for her, and scheduling for me) has solved the problem and we all eat together in peace.
Good luck!