We're not talking about bacteria:
Taken from any number of gluten free info sites.
Dedicated/Non-Dedicated Production Lines
This classification applies to the production line on which a particular product is manufactured. When a product is manufactured on a dedicated line, the equipment used to produce that product will only come into contact with elements that are explicitly included in that product's ingredients (i.e. if "product A" is produced on a dedicated line, then there is no chance of contamination from the ingredients explicitly contained in "product B.") Even if a different product is run on this dedicated line, the line will be thoroughly cleaned between production runs to ensure that there is no possibility of cross-contamination.
If a product is not run on a dedicated line, this means that a chance of contamination by foreign elements (not explicitly contained in the product's ingredients) is possible. In this scenario, potential contaminating substances may or may not be present in trace amounts, depending on the ingredients contained in other products run on the same line. When making a decision on whether or not to eat a product that is not run on a dedicated line, one should carefully consider one's allergies, taking into account the severity of the allergy/allergies. Since contaminating elements are potentially only present in trace amounts, the product in question may be suitable to an individual with only mild allergies/sensitivities. Individuals with more severe allergies/sensitivities should avoid products with potential contaminants altogether.
Click on the "allergen" tab for any individual product for detailed information on that product's allergen profile.
That said, I think there tends to be less of a problem in homebrewing for cross-contamination following cleaning & sanitizing because there is less equipment involved, and much of it is easily cleanable.
While best to keep a separate filling line, autosiphon and filler, due to crevices, the other components are:
Brewpot, fermenters (bucket/carboy/keg), wort chiller.
Three things with fairly smooth surfaces that will clean easier than multiple tubes, multiple nozzles, etc.
And really... it all depends on the recipient's tolerance level. Some people have to avoid products that share a line since they may be ultrasensitive. Some people are fine with a shared line since if they get a tiny bit, they're ok, and its when they have a significant amount that they have a reaction.