MTO does not work agianst stock, it only produces a new manufacture order which will be used to produce the master BOM.

If you want to check what stock you have when running MO or SO you need to use replenishment rules and manufacture routing, not MTO routing.

Edit:

From v14.0+ MTO does check for quantities in stock, and takes from stock IF (and only if) the order can be fullfilled from stock, ELSE it triggers a buy/manufacture order for the exact quantity needed (ignoring any stock).