1st – the aluminium foil will be fine within the glass, it does not have the strength to break the glass. I have stopped using it, because for me it always seems to go brown.
Paints – It depends on what you are using. If you are using anything other than vitreous paints, yes they will burn out. Vitreous paints will stand up to fusing, although the glass stainer’s enamels tend to thin in colour.