it won't be a problem. you will find ways to compensate. i brew small batches and the next one will actually be a modified biab, actually mash in a bag. i have a 22 quart electric roaster oven that i intend to mash in. lift the grain bag out and rinse it over a grate, then crank up the heat to boil.Nothing wrong with kegging 3 gallons in a 5 gallon keg. I do it all the time since I brew 3 gallon batches exclusively.
dave R. do you bottle or keg. i have been playing with different ways of kegging 1-3 gallon brews and haven't found a perfect fit yet