Does this use the game's real drop rates?
No, and no site has them — the developer has not published drop rates. This planner works from things that can be observed directly: which rarity band an OVR falls into, how scarce goalkeepers are, and how deep each category is.
Why does it keep telling me to fix my goalkeeper?
Because goalkeepers are the scarcest position in the game at 15 cards out of 214, and unlike outfield players they cannot be covered by a card cycling into the slot from another position.
Should I stop taking high cards from other categories?
Once you have committed to a Chemistry category, largely yes. Official art shows matched players 14 to 17 points above their base rating, which is bigger than almost any single-card upgrade you would be trading it for.