I flipped the stem this week to bring the handle bars up and a little closer, been out on it for a two hour ride and definitely more comfortable.
I am pretty inflexible and tended to suffer from lower back pain on long, hilly rides. For years I had a medium length stem on my Cannondale CAAD5, flipped for the same reasons that you did it.
Then a couple of years ago I was on holiday in Scotland and borrowed my cousin's bike. It is also a CAAD5, the same size as mine, but it has an unflipped longer stem and about 1 cm less spacers under it. I thought that I would struggle with the longer, lower position but in fact I much preferred it. I have now replicated the position on my bike and found it a big improvement.
I think the reason is that my body proportions are a bit odd. I am 6' 1" tall but don't have particularly long legs (32" IL). (There are plenty of men 3 inches shorter than me with legs that long.) I make up the height with a long torso.
My former short, upright position was putting unwanted curvature on my lower back. Now I am stretched out I am more comfortable. It just goes to show how individual correct bike fit is.