Nay-nay, there's nothing wrong with making the bechamel firs and then leaving aside before putting the veg into the TM to cook.
Alternatively, you can mix the flour & butter together and drop small bits in while still cooking near the end then cook another 5 or 10 mins to cook out the flour and add the milk?
The flour and butter mixture is called
Beurre manie and useful as a thickener. But as CP63 says - if you don't cook it long enough it will have a raw flour flavour.