I could be wrong, but I was under the impression that they used a silicone based glue, just like in glass aquariums. Like I said before I'm no expert on acrylics or acrylic glue.
While answering you, I looked this subject up on the net. It appears that something called WeldOn is being used to build and repair acrylic tanks. It appears to be what you are talking about and harmless to fish when dry. Seems kind of strange considering how toxic that the warnings say it is.
They say that silicone is OK for light duty jobs where you are attaching something like silicone baffles to glass, but acrylic glue is necessary for plexiglas tanks. The jury is out on whether you can use acrylic glue to repair scratches in glass, unless you've had some success in that regard. From what you said above, it seems that you do.
But back to the topic at hand. I found the following non-toxic method on the web:
1) Apply a white, non-gel toothpaste to a light scratch on a glass surface. Make sure the entire scratch is covered liberally with the toothpaste.
2) Allow the toothpaste to harden. This should only take a few minutes.
3) Wipe off the toothpaste with a soft cloth. Buff the scratched area in one direction to avoid added new marks to the glass. In most cases, you will see that the scratch is gone once all of the toothpaste has been removed.
4) Mix together a paste from white vinegar and ground mustard seed to tackle slightly deeper glass scratches. Ground mustard seed is available in the spice aisle of your local supermarket. Start with a tablespoon of the dry mustard and add a few drops of vinegar at a time to avoid making the mixture too wet.
5) Slather the mustard-and-vinegar paste onto the scratch, allow it to dry and buff off with a cloth.
Sounds interesting. This is a method for removing scratches from automobile glass. You might try that. You would think that the toothpaste wouldn't hold up, but I know from experience that when it dries it is like concrete.