If you put 5 gallons exactly into your fermenter, you can’t expect to get 5 gallons of finished beer out. There is trub and waste produced by the yeast. During your boil, you get solids that fall out, called “hot break.” Then when you cool the beer from boiling to pitching temp more solids will drop out, called “cold break”. In addition to that, you add hops during the boil which also collect and fall out. Even if you whirlpool and settle you will not get all the trub. Then the yeast reproduces and settles out.
There can be a fair amount of beer loss from waste. I get around it by adding an extra half gallon to all my batches. If I brew a 5 gallon batch, then I would plan a 5.5 gallon batch in my software, plan to collect 6 gallons from the mash, boil down to 5.5 gallons and 5.5 gallons would go into my fermenter. Then if I rack to a secondary, I could get a full 5 gallons there. The losses from any settlling in a secondary will be much less than kettle losses and primary losses. You might lose one 12 oz bottle from any secondary.
I haven’t bottled a 5 gallon batch for a very long time, but I recall it was always just about 50 bottles. 128 oz in a gallon x 5 gallons = 640 oz / 12 oz bottles = 53 on paper but I found it was never that because you don’t get every drop.