Hopefully a professional chimes in but I believe it does imply that he ate it all. Your example isn't one to one because you refer to it as "I ate chili" instead of "I ate it". Same way people wouldn't be confused if he had said, "He ate Salmon that night but" .
Similar examples:
I painted it last night. (Painted a painting)
I beat it last night. (Beat a game)
I ran it last year. (Ran a marathon)
"Where's the chili?" "Oh, I ate it last night, sorry." (Ate the chili)
"Mmm, this chili is good, isn't it?" "Sure is, I had some last night." (Ate some of the chili)