My understanding is that the "can't ... too ..." phrase is, in essence, an emphatic and positive way of expressing ideas, though there is a negative word in it. It can be paraphrased as "the [comparative]..., the [comparative]..." or into other patterns of emphasis. Sounds vague. Let's look at the following sentences.

(1) "We can't be too careful in choosing friends."
This means the more care we exert in choosing friends, the better it is.

(2) "We can't emphasize the importance of health too strongly."
This is an emphatic way of expressing the importance of health.

Now my question is:
Does the "can't ... too ..." phrase ALWAYS have the positively emphasized connotation, in other words, can't it sometimes have its literal meaning?

Look at my creation, please.

(Wife talking to husband about their children eating something voraciously)
Wife: I am afraid they are eating too much.
Husband: Don't worry, honey. They can't eat too much. (My intended meaning: Their stomachs have the limits.)

Is my creation itself faulty?
You are correct. Sometimes it is meant literally. These sentences are rather ambiguous and you will have to use context and common sense to decide which meaning is relevant, unless there is a rule I cannot think of.

More examples:

They can't climb too high.

I can't eat too much chocolate (definitely ambiguous in my case!).
Please move this posting to General English Grammar Questions, if you think it's out of place.
 nona the brit's reply was promoted to an answer.