Yes, you need to cover them with glass first. You also need to etch the Aluminum to ensure a strong, lasting bond.
You will probably find it easier to tack the frame first and then cover the exposed metal with glass. You can then use the glass as a base structural layer by extending it onto the frame. A few pieces of glass extending from the down tube between the chainstays and up the back of the seattube and a few more from the downtube and split to overlap onto the chainstays will tie that area together. It is easiest to buy a few rolls of fibrerglass tape for this application. The finished edges of tape reduce the problem of the glass weave coming undone.
The exception may be the dropouts. If you insert them into the bamboo then the carbon wrap will only reinforce the bamboo without actually contacting the metal.
You of course have the option of sleeving everything into bamboo first which will eliminate the necessity of the insulating layer.
Your lugs can look a bit bulky if you go that route unless you use the thinnest walled bamboo.