This is an unusual and probably jargony usage of encode. It's close to what is described here (emphasis added by me):
If you encode a message or some information, you put it into a code or express it in a different form or system of language.
Here, the "message" is the idea the manager wants to convey, which he encodes into a particular system of language - namely, a string of spoken words. Then the listener decodes the spoken words into an idea in their own mind.
The full text you link to is pointing out that the final idea in the listener's mind could be very different from the original idea in the speaker's mind because the steps of encoding (turning an idea into words) and decoding (turning words into an idea) are subject to individual biases.
Again, this is a very unusual way of describing spoken communication - encode is not commonly used this way.