As others have said, there's nothing inherently wrong with topping off past 5 gallons but you will alter the profile of the beer. You'll change your OG and probably your final IBUs. Probably not the color with just a quarter of a gallon, but you'll have a different-tasting beer in exchange for like two extra bottles of beer.
Losing volume between the fermentation and bottling is pretty normal, so I wouldn't sweat it too hard. The main thing you'll want to focus on is reaching a target OG. If you're doing that and you're hitting 4.75 gallons routinely then you're doing it right.
If it's really something that bothers you, use something like BeerSmith 2 or any of the various calculators to find your optimal pre-boil gravity and change your recipe accordingly by adding more extract. I think you're better off avoiding adding extract after the boil. Also, you might want to use DME rather than LME for this since DME's typically aren't hopped and won't affect your color, where LME's will make your beer darker and hoppier.