If the question is specifically related to "factory glass" and if that also implies a reasonable quantity of available similar items, then I'd buy only a good piece.
But I have several items that have minor, and not-so-minor damage. Some were already repaired with careful grinding which did not detract from the overall look but at the same time is clearly visible for later owners to note.
I also have some pieces (paperweights) that have severe damage and there is no possible way to have them repaired. To me, these are just extreme versions of the ones bidda and Leni mentioned, that are useful for learning. In fact, some of my broken pieces were purchased because they have features that add to the academic aspect of my collecting and hopefully help to tie together loose ends of history. For those items, I am prepared to pay more than just a "damaged price"!
I have never purchased anything with the aim of monetary profit, so my "value" of an item lies in how it can help me understand something as well as it being a pleasing piece of glass artwork. So, damage is often a secondary consideration for me.