You don't come up short on secondary, it is what it is. If an extract brewer and throw everthing into primary than you make adjustments to make your mark. Any loses after that is the cost of doing business. Using a full boil volume you can make adjustments in the kettle before transfering to primary. Adding water to secondary to keep volume up just dilutes your projected results and will not yeild consistancy from recipe to recipe. When I first started brewing and was told it was a 5 gallon batch then that's what I expected to be bottled. It took me forever to except my final volume would be less than that and had many bottles containing sediment that should have been left behind.
If still determined to top off secondary, knock yourself out. If final volume makes you happy, I no doubt understand. I still refuse to waste any byproduct produced in the brewing process. Left over sediment from primary (though not all) is used as my yeast starter for the next batch, bumping up my primary volume. So far six generations without problems. Water expelled from wort chiller is collected and dumped in the washing machining, which means brew day is laundry day. Wort samples for gravity readings is frozen and saved for starters. It is what you make of it.