I will top off the fermentor with one-half to three-quarters of a gallon water for a 5 gallon recipe when I start with 2.5 gallons water in the boil kettle. The variable amount of top off water is due to the amount of boil off and the amount of water added with LME when LME is used in the recipe.
The most number of bottles filled for a 5 gallon brew has been 50. 600 ounces of beer out of 640 total ounces for 5 gallons. Most often it is 48 to 49 filled bottles with some slop over and 4 ounces left in the bottling bucket.. I have the carboy tilted forward when siphoning. This helps to keep the siphon from getting too near the yeast/trub layer and drawing up excess yeast. I intend to leave some beer in the carboy to keep the yeast covered until harvest.
I boil with the lid mostly on the kettle. I do this to be able to reduce the amount of heat applied to the bottom of the kettle and still maintain a gentle boil. Less applied heat may reduce the amount the extract is darkened due to the Maillard Reaction. I do periodically wipe the heavy condensation from the underside of the lid. Letting this condensation drip back into the kettle can retain DMS if it does form during the boil. DMS precursors can reform during the boil with Pilsen malt extract and possibly some other extracts. (First time I noticed DMS was during the boil for a Hefeweizen.)