Yes, if a player earns an Extra Walk as a Day Bonus and already has 3 cards in that day's column, the Extra Walk becomes a fourth card in that column. This is a specific exception to the usual maximum of 3 cards per day.

This is supported by the following rule:

• "Each day can have a maximum of 3 cards in its column. (Extra Walk cards, which are explained on page 8, are the exception.)"
  (page 6)

Further, the rules for Extra Walk state:

• "When taking this bonus, a player simply takes a face-down card (without looking at it) from either the Tokyo or Kyoto deck and places it face-down in their itinerary in the day for which they earned the bonus, so that there are 4 cards in this column, otherwise respecting placement rules."
  (page 8)

Summary

• The Extra Walk card is placed as a fourth card in the column, exceeding the normal 3-card limit for that day.
• This exception only applies to Extra Walk cards.

Sources:
page 6, page 8

Source: Base Rules (pp. 10, 15, 6, 7, 8)