There are multiple cyanoacrylates (superglues) on the market, and they will give very different results. Gel superglue formulations usually have some type of rubber or fumed silica additive to make them thicker, and the additive usually doesn't burn out. That's probably where the "superglue leaves a mark" originates. Usually the cheapest possible superglue is best for temporary glass holds because it'll mostly be additive-free.
The glue will burn out around 700F or so, so it shouldn't be used to position the glass against gravity. I disagree, however, that it should never be used. I buy cheap superglue by the carton and use it in everything from temporary casting assemblages to making glass boxes for frit panels to tack-fusing. It is the best way I know to hold wobbly pieces in place until you can assemble the rest of the glass around it.
Some tips for using superglue:
- You are more likely to get whitish residues if you let moisture get to the superglue while it's drying, so keep the glass surfaces as dry as possible and don't put a superglue-assembled piece on a wet kiln shelf.
- Always try to put the glue under opaque or dark glasses, just in case something goes wrong.
- Use the smallest amount possible. Don't flood an area with glue and lay the glass on top - that will almost always leave too much glue on the glass. Instead, I assemble the glass and put a drop of glue right where the two glasses join. Capillary action sucks just the right amount of glue into the joint.
- If you wipe excess glue away with acetone, be careful about which acetone you're using. Some types (such as nail polish remover) can have additives that leave residues on the glass and make the problem worse. If the glue is in a readily accessible area, it is usually better to wait for it to dry, then peel it off the glass with a razor blade. Only use acetone where there's texture or something else that makes the glue difficult to remove. And in any case, don't worry much about removing superglue right on the surface--it will burn off.
- Superglue joints will NOT support the weight of your glass, i.e., never, ever lift your assemblage by a superglued-on piece of glass. Common superglue is actually a lousy glue for glass--which is why it works as a temporary hold.