You're bottle conditioning, right, not filling from kegs using a counter pressure bottle filler?
If you're bottle conditioning, I don't think it's going to matter if the beer comes up to temperature before or after you bottle. It's going to need to get up to temperature for the yeast to carbonate, assuming you're using an ale yeast. Whether that happens before or after it's bottled it unimportant, I think. Even if you're using lager yeast, you'll need to get the temperature up above your cold crash temperature to get it to carbonate.