I am assuming you've consulted with a pediatrician, and from that standpoint your son is well and gaining weight. If this is so, and you're really worried that something is wrong, I'd get the second opinion and see a GI specialist.
I myself had GI problems as a child, and as result didn't eat very well. I gravitated toward soft foods for a really long time because I had an underdeveloped stomach and intestines which went undiagnosed for a long time. It wasn't until I was sent to a specialist the problem was tracked down.
Though a problem at birth, it wasn't a permanent one. I eventually outgrew the problem, and eventually ate like everyone else. But in the interim, it was a real nightmare because my mother was at her wits end trying to keep me healthy and my immune system up to par.
In the interim of getting to the specialist, if you're son prefers being spoon fed by you, and only wants puree and rice cereal so be it. If it will get him to eat, then there really is no problem. Food is food whether it's ground up or whole. If it's a problem that he's not feeding himself while you and your spouse are eating, just feed him first. Then you and your husband can eat without worry after.
Also consider if he's filling up on too much milk and as a result is just not hungry for meals. Be sure to feed him food first, then milk later. Also consider trying to serve milk only at meal times too.
Don't discount a mild illness, GIRD, or food allergies. He may not be eating because the food isn't agreeing with him or he is not well. Many food allergies don't manifest in skin breakouts, but in other ways like gastrointestinal disturbances, bloating, and nausea.
As for whether he's developing dependence or bad habits, I think he'll eventually outgrow this needing to fed business. When he's older, and if he's in a preschool or daycare setting or with other friends or siblings, he'll want to be like everyone else, and will be all to eager to feed himself.
It may be a phase, or it may be symptomatic. I'd just do what you need to do for now to maintain his health, strength and your peace of mind until you get a second opinion from a specialist.
Good luck. Hope this helps.