They are identical currently between the two factories. Same battery, same castings. No current Model Y sold the US has front casting anymore. Austin now also builds the Performance as well.
I believe Quicksilver paint was initially only from the Austin factory but now that they added Quicksilver to Model S/X, that means Fremont now has the ability to paint Quicksilver. Not sure if Model Y uses the same paint line as S/X at Fremont though.