Based on the Appraisal text that is displayed when you have an exceptionally large or small Pokémon, it appears that the Pokédex entry is a height/weight reference, giving the average height/weight of that species.
Here is a chart with all of the Appraisal quotes.
Note: These are quotes from Blanche, the leader of Team Mystic:
Phase #3: Pokémon Size Size
- Your [Pokémon Name] is tinier than any we have on record. Astounding. XS
- Your [Pokémon Name] is below average in size. Small
- Your [Pokémon Name] is above average in size. Large
- The size of your [Pokémon Name] is… colossal. This is indeed exceptional. Fascinating! XL
Since height/weight have no bearing on a Pokémon's IVs or CP, these don't really mean anything for your Pokémon other than just being a fun fact.