Hi, I don't know if this will help, but my DD (15 months) hates, absolutely HATES, having to eat from a plate or in a high chair. She wants to be on the move, and she wants to eat from my plate. I decided it's not worth the battle--she gets a plate to eat off of (and sometimes she'll eat a little bit, usually a few bites, but sometimes a bunch), and I sit on the floor/chase her around and offer food till I think she's full. It works. My mom thinks it's weird, but hey, my DD gets enough food, and we don't have any power struggles over it. (She's skinny but has always been that way, and growing steadily.)
I also offer healthy snacks if I get the slightest hint that she's hungry, and I often will leave a few bites of bread or pear or veggies on a plate where she can cruise by later and grab a handful when she happens to see them.
Oh, and my DD is crazy about Cheerios, which I do not consider a healthy snack, so we celebrate Cheerio Day. She gets Cheerios on Fridays--as many as she wants. Now she knows the days of the week, and she gets reeeeeally excited about Fridays. :)
Good luck! Isn't it frustrating trying to feed a toddler? Your son's food intake doesn't sound like any less than my DD's, but I have to admit that she still nurses a lot. Is he growing steadily (has he always been in the 3rd percentile for weight)? Will he eat high-calorie stuff like avocado, cheese or almond butter? My DD is crazy about toast with almond butter.