Yes, Lew, those are some good points about a built-in. Here are some good points about why I believe separates can sound better if done properly.
1- Power supply modulation of the phono stage by the line stage.
2- keeping the phono section off when not needed
3- ability to use the phono section closer to the source
4- more real estate in the box for loading options, dual MC sections etc.
5- it actually sounds better though this is the territory of diminishing returns. Many people may well be better off putting the extra cost to solving other issues in their systems.