A larger frame will normally have a longer seat tube, a longer top tube AND a taller steering tube so its hard to say if there would be any advantage. Comfort is the real decider.

On the other hand you mentioned the bike had a quill type stem, and those come in various sizes (heights) and reaches, as well as adjustable models. Same for handlebars. Lots of styles with different amounts of rise and sweep. No reason you can't find a combo that does the trick.

If its an easy swap - you might even get it done before the bike leaves the store for a minimal cost.